├── .gitignore ├── README.md ├── data ├── ebola │ ├── ebola.fasta │ ├── ebola.metadata.csv │ └── ebola.nwk ├── h3n2_na │ ├── h3n2_na_20.fasta │ ├── h3n2_na_20.metadata.csv │ ├── h3n2_na_20.nex │ ├── h3n2_na_20.nwk │ ├── h3n2_na_20.phylip │ ├── h3n2_na_200.fasta │ ├── h3n2_na_200.metadata.csv │ ├── h3n2_na_200.nwk │ ├── h3n2_na_20_aa.fasta │ ├── h3n2_na_500.fasta │ ├── h3n2_na_500.metadata.csv │ └── h3n2_na_500.nwk ├── tb │ ├── lee_2015.informative_sites.fasta │ ├── lee_2015.metadata.tsv │ ├── lee_2015.nwk │ ├── lee_2015.vcf.gz │ └── tb_ref.fasta └── zika │ ├── zika.country_weights.csv │ ├── zika.fasta │ ├── zika.metadata.csv │ ├── zika.nwk │ └── zika.phylip ├── figures ├── clock_plot.png ├── ebola_outliers.png ├── ebola_skyline.png ├── timetree.png └── tree_and_clock.png └── scripts ├── ancestral_sequence_inference.py ├── ebola.py ├── relaxed_clock.py └── rerooting_and_timetrees.py /.gitignore: -------------------------------------------------------------------------------- 1 | 201* 2 | *results 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Collections of examples of phylogenetic analysis with [TreeTime](https://github.com/neherlab/treetime) 2 | 3 | There are three different ways of using TreeTime: 4 | 1. as a python module as part of [python scripts and programs](#treetime-in-python-scripts) 5 | 2. [via a set of command-line tools](#command-line-usage) 6 | 3. via the webserver at [treetime.ch](http://treetime.ch). 7 | 8 | The documentation of TreeTime is now hosted on readthedocs: [![readthedocs](https://readthedocs.org/projects/treetime/badge/)](https://treetime.readthedocs.io/en/latest/) 9 | 10 | 11 | ![Molecular clock phylogeny of 200 NA sequences of influenza A H3N2](https://raw.githubusercontent.com/neherlab/treetime_examples/master/figures/tree_and_clock.png) 12 | 13 | ### Command line usage 14 | The general pattern to use TreeTime to infer timetrees via the command line is 15 | ```bash 16 | treetime --tree mytree.nwk --aln mysequences.fasta --dates metadata.csv 17 | ``` 18 | In addition, there are number of subcommands for related tasks. 19 | Please see the following pages that explain usage for different cases: 20 | * [timetree estimation](https://treetime.readthedocs.io/en/latest/tutorials/timetree.html) 21 | * [estimation of substitution rates](https://treetime.readthedocs.io/en/latest/tutorials/clock.html) 22 | * [ancestral sequence reconstruction](https://treetime.readthedocs.io/en/latest/tutorials/ancestral.html) 23 | * [homoplasy analysis](https://treetime.readthedocs.io/en/latest/tutorials/homoplasy.html) 24 | * [discrete traits and mugration models](https://treetime.readthedocs.io/en/latest/tutorials/mugration.html) 25 | 26 | 27 | ### TreeTime in python scripts 28 | A minimal script to run TreeTime would look something like this 29 | ```python 30 | from treetime import TreeTime 31 | from treetime.utils import parse_dates 32 | 33 | dates=parse_dates('metadata.csv') 34 | tt=TreeTime(tree='mytree.nwk', aln='mysequences.fasta', dates=dates) 35 | tt.run(root='best') 36 | ``` 37 | More detailed examples can be found in the following set of scripts: 38 | * [rerooting and timetree inference](scripts/rerooting_and_timetrees.py) 39 | * [ancestral sequence reconstruction](scripts/ancestral.py) 40 | * [relaxed clock models](scripts/relaxed_clock.py) 41 | * [an analysis of 2014-2016 Ebola virus sequences](scripts/ebola.py) 42 | -------------------------------------------------------------------------------- /data/ebola/ebola.metadata.csv: -------------------------------------------------------------------------------- 1 | name, date 2 | EM_COY_2015_015982, 2015.30 3 | G3676, 2014.40 4 | EM_COY_2015_015980, 2015.30 5 | G3670, 2014.40 6 | CON-10590, 2015.61 7 | NM042, 2014.42 8 | EM_079497, 2014.26 9 | 2507_C2_10080_EMLK, 2015.06 10 | G3677, 2014.40 11 | LIBR10180, 2014.77 12 | KG12, 2015.40 13 | G3770, 2014.44 14 | Makona-G5114.1, 2014.63 15 | EM_COY_2015_023747, 2015.69 16 | EM_FORE_2015_1023, 2015.49 17 | J0170, 2014.86 18 | EM_FORE_2015_1437, 2015.53 19 | NZG_0422, 2016.25 20 | EM_079429, 2014.25 21 | 2507_C2_10123_EMLK, 2015.07 22 | Makona-G4419.1, 2014.54 23 | NZG_0358, 2016.22 24 | EM_079422, 2014.23 25 | EM_079423, 2014.23 26 | EM_079421, 2014.24 27 | EM_079775, 2014.39 28 | REDC_GUI_2015_01165, 2015.63 29 | DML12120, 2015.16 30 | CON-8811, 2015.48 31 | 1708_C2_MK2656R2, 2015.17 32 | 1507_C1_18706_EMLH, 2015.53 33 | Makona-G5112.1, 2014.63 34 | EM_076403, 2014.82 35 | 0507_C2_MK0664, 2014.99 36 | Makona-G4416.1, 2014.54 37 | EM_000501, 2014.70 38 | EM_COY_2015_016449, 2015.36 39 | G3682, 2014.40 40 | EM_COY_2015_015972, 2015.30 41 | 1807_C2_14795_EMLK, 2015.31 42 | REDC_GUI_2015_01408, 2015.67 43 | EM_080253, 2014.52 44 | J0076, 2014.79 45 | V633, 2014.61 46 | EM_000218, 2014.68 47 | LIBR10202, 2014.65 48 | Makona-G4423.1, 2014.54 49 | EM111, 2014.42 50 | EM110, 2014.42 51 | LIBR10035, 2014.62 52 | V20143415, 2014.83 53 | 0809_C1_19560_EMLK_E, 2015.68 54 | 3004_C1_KT5974, 2015.20 55 | EM_FORE_2015_1313, 2015.52 56 | 0807_C1_14750_EMLK, 2015.30 57 | 0806_C1_PL7376, 2015.40 58 | 1507_C2_15674_EMLK, 2015.49 59 | 3004_C2_KT5382, 2015.15 60 | EM_079405, 2014.24 61 | EM_004192, 2014.97 62 | J0019, 2014.73 63 | 1807_C2_14830_EMLK, 2015.32 64 | EM_079408, 2014.24 65 | EM_000934, 2014.74 66 | EM_076322, 2014.80 67 | Makona-G4415.1, 2014.54 68 | EM_078608, 2014.92 69 | 2607_C2_12781_EMLH, 2015.26 70 | J0124, 2014.84 71 | EM_079587, 2014.30 72 | 1805_C1_MK2724, 2015.17 73 | 2507_C1_77795_EMLK, 2015.04 74 | 0507_C1_PL4283, 2015.17 75 | NZG_0393, 2016.24 76 | LIBR10217, 2014.74 77 | J0056, 2014.77 78 | 1507_C1_18650_EMLH, 2015.52 79 | J0053, 2014.76 80 | LIBR0430, 2014.92 81 | Makona-G4942.1, 2014.61 82 | REDC_GUI_2015_02242, 2015.81 83 | IPDPFHGINSP_GUI_2015_5117, 2015.25 84 | 2607_C2_12855_EMLH, 2015.28 85 | 0806_C1_KT4715, 2015.10 86 | Combined_PL9192, 2015.53 87 | 1807_C2_14846_EMLK, 2015.32 88 | J0123, 2014.83 89 | EM_FORE_2015_2878, 2015.81 90 | G3735, 2014.43 91 | G3734, 2014.43 92 | Makona-G4422.1, 2014.54 93 | LIBR10017, 2014.63 94 | EM_FORE_2015-1971, 2015.62 95 | 1009_C1_20525_EMLK, 2015.68 96 | EM_COY_2015_014100, 2015.23 97 | EM_FORE_2015_1076, 2015.50 98 | 1807_C1_15327_EMLK, 2015.43 99 | Makona-G4348.1, 2014.52 100 | Makona-G4702.1, 2014.59 101 | 3004_C1_KT5858, 2015.19 102 | 2507_C1_77767_EMLK, 2015.04 103 | EM_079815, 2014.40 104 | Makona-G3972.1, 2014.48 105 | V20140024, 2014.63 106 | Makona-G4437.1, 2014.55 107 | 0106_C2_KT2316, 2014.92 108 | 1708_C1_12705_EMLH, 2015.24 109 | 2208_C2_18659R_EMLH, 2015.52 110 | EM_004437, 2015.01 111 | 1209_C1_20573_EMLK, 2015.69 112 | EM_080213, 2014.50 113 | V768, 2014.65 114 | 1805_C1_MK2255, 2015.14 115 | REDC-GUI-2015-00502, 2015.53 116 | EM_074548, 2014.60 117 | 0305_C2_PL4570, 2015.19 118 | EM_074461, 2014.59 119 | 2507_C2_10353_EMLK, 2015.10 120 | 1807_C1_PL9150R, 2015.53 121 | LIBR0093, 2014.85 122 | LIBR0090, 2014.85 123 | EM_079424, 2014.23 124 | IPDPFHGINSP_GUI_2015_5038, 2015.25 125 | V1561, 2014.80 126 | 0205_C2_PL5868, 2015.26 127 | V1039, 2014.71 128 | J0037, 2014.75 129 | EM_079685, 2014.36 130 | EM_079681, 2014.36 131 | EM_080265, 2014.53 132 | J0129, 2014.84 133 | 1007_C2_PL4105, 2015.16 134 | 1807_C2_10398_EMLK, 2015.11 135 | EM_079517, 2014.27 136 | EM_079514, 2014.27 137 | J0127, 2014.83 138 | 0806_C1_KT4677, 2015.09 139 | LIBR10077, 2014.65 140 | V509, 2014.56 141 | EM_076610, 2014.84 142 | 0106_C2_PL7375, 2015.40 143 | EM_079702, 2014.36 144 | EM_076948, 2014.87 145 | 1807_C1_PL8310b, 2015.47 146 | EM_GUI_2015_004674, 2015.23 147 | 0205_C1_PL5428, 2015.23 148 | EM_000219, 2014.68 149 | EM_079578, 2014.29 150 | 1507_C1_18647_EMLH, 2015.52 151 | 1805_C1_MK2382, 2015.15 152 | A023888, 2015.70 153 | G3686, 2014.40 154 | EM_079749, 2014.38 155 | IPDPFHGINSP_GUI_2015_4909, 2015.24 156 | Makona-G5853.1, 2014.72 157 | EM_004555, 2015.06 158 | J0081, 2014.79 159 | Makona-G5059.1, 2014.63 160 | EM_079630, 2014.33 161 | G3814, 2014.45 162 | 1807_C2_14763_EMLK, 2015.30 163 | 0208_C1_MK10173, 2015.58 164 | EM_079542, 2014.28 165 | 1507_C1_13268_EMLH, 2015.47 166 | 0205_C2_PL6086, 2015.28 167 | DML25411, 2015.19 168 | 2208_C2_18687R_EMLH, 2015.53 169 | EM_079549, 2014.28 170 | EM_COY_2015_016617, 2015.37 171 | Makona-G4347.1, 2014.53 172 | 1708_C1_13031_EMLH, 2015.38 173 | LIBR0177, 2014.87 174 | V20144820, 2014.87 175 | 1309_C2_MK13013, 2015.70 176 | G3782, 2014.45 177 | Makona-G4312.2, 2014.53 178 | 1507_C1_18636_EMLH, 2015.51 179 | EM-FORE-2015-664, 2015.42 180 | 1009_C1_20547_EMLK, 2015.68 181 | 1507_C2_MK0575, 2014.99 182 | 1009_C1_20524_EMLK, 2015.68 183 | 0807_C1_PL4119, 2015.16 184 | EM096, 2014.40 185 | DML24573, 2015.05 186 | J0015, 2014.73 187 | J0016, 2014.74 188 | 0205_C2_PL6049, 2015.27 189 | 2607_C1_592_EMLH, 2015.10 190 | EM_079434, 2014.25 191 | EM_COY_2015_017787, 2015.45 192 | EM_COY_2015_017018, 2015.40 193 | LIBR10110, 2014.63 194 | Makona-G5985.1, 2014.73 195 | EM_COY_2015_016456, 2015.36 196 | G3840, 2014.46 197 | EM-FORE-2015-1414, 2015.53 198 | 1807_C1_15421_EMLK, 2015.45 199 | 1007_C2_MK1000, 2015.02 200 | 2906_C2_KT5034, 2015.12 201 | V20140729, 2014.69 202 | EM_COY_2015_022059, 2015.50 203 | Makona-G4236.1, 2014.52 204 | V1211, 2014.75 205 | 1807_C1_PL9199Rb, 2015.53 206 | 2507_C1_77748_EMLK, 2015.03 207 | LIBR0505, 2014.94 208 | Makona-G4972.1, 2014.62 209 | 2208_C2_15207R_EMLK, 2015.41 210 | LIBR10270, 2014.65 211 | LIBR10271, 2014.65 212 | EM_079388, 2014.57 213 | 2507_C2_10212_EMLK, 2015.08 214 | Makona-G3889.1, 2014.46 215 | 1708_C1_MK0491R, 2014.97 216 | 0807_C1_PL4813, 2015.20 217 | G3769, 2014.44 218 | V20143036, 2014.81 219 | J0161, 2014.85 220 | EM_COY_2015_016531, 2015.36 221 | J0167, 2014.85 222 | J0168, 2014.86 223 | J0169, 2014.85 224 | CON-10512, 2015.61 225 | EM_079413, 2014.24 226 | EM_079412, 2014.24 227 | CON-10193, 2015.59 228 | EM_079410, 2014.24 229 | EM_079414, 2014.24 230 | FCH_731, 2015.73 231 | FCH_730, 2015.73 232 | LIBR10053, 2014.75 233 | CON-8559, 2015.47 234 | LIBR10196, 2014.65 235 | 2507_C2_10084_EMLK, 2015.06 236 | 2807_C2_567_EMLH, 2015.09 237 | V653, 2014.62 238 | EM_000921, 2014.74 239 | V20146578, 2014.98 240 | EM_078556, 2014.91 241 | LIBR0605, 2014.97 242 | 0807_C1_PL4123, 2015.16 243 | V20143648, 2014.84 244 | LIBR1221, 2015.09 245 | EM_FORE_2015_1140, 2015.50 246 | LIBR10056, 2014.73 247 | Makona-G3917.1, 2014.47 248 | EM095, 2014.39 249 | 0809_C1_020484_EMLK_A, 2015.67 250 | EM_NG_2016_029417, 2016.22 251 | EM_004059, 2014.97 252 | 2906_C1_PL4483, 2015.18 253 | J0112, 2014.83 254 | J0042, 2014.76 255 | 2807_C2_77693_EMLK, 2015.02 256 | 2906_C1_PL8172, 2015.46 257 | 1807_C1_14888_EMLK, 2015.33 258 | EM_079464, 2014.25 259 | Makona-G4264.1, 2014.52 260 | REDC-GUI-2015-00497, 2015.53 261 | LIBR10205, 2014.71 262 | EM_NG_2016_029366, 2016.21 263 | EM_NG_2016_029364, 2016.21 264 | Makona-G4252.1, 2014.52 265 | 2507_C1_10022_EMLK, 2015.05 266 | EM_COY_2015_015815, 2015.28 267 | EM_FORE_2015_697, 2015.43 268 | Makona-G4250.1, 2014.52 269 | 0208_C1_77679_EMLK, 2015.02 270 | G3820, 2014.45 271 | G3823, 2014.45 272 | LIBR0073, 2014.85 273 | G3827, 2014.45 274 | EM_COY_2015_017574, 2015.44 275 | Makona-G5982.1, 2014.73 276 | 1706_C1_PL7709, 2015.43 277 | REDC_GUI_2015_01323, 2015.65 278 | EM_COY_2015_016642, 2015.37 279 | FCH_729, 2015.73 280 | LIBR0622, 2014.97 281 | LIBR0624, 2014.97 282 | 3004_C2_KT5320, 2015.15 283 | NZG_0381, 2016.23 284 | EM_COY_2015_017174, 2015.41 285 | CON12930, 2015.78 286 | EM_076534, 2014.83 287 | V20144192, 2014.85 288 | 3007_C2_77581_EMLK, 2015.01 289 | J0021, 2014.74 290 | J0020, 2014.73 291 | 0806_C2_KT4631, 2015.09 292 | EM_COY_2015_017135, 2015.41 293 | 2605_C2_PL5534, 2015.24 294 | FCH1785_S, 2015.70 295 | 2807_C2_77712_EMLK, 2015.02 296 | LIBR10237, 2014.52 297 | J0137, 2014.83 298 | EM_079914, 2014.44 299 | J0134, 2014.83 300 | 0205_C2_PL6070, 2015.27 301 | 1706_C1_PL7801, 2015.44 302 | 2208_C1_PL4256R, 2015.17 303 | 1507_C1_18660_EMLH, 2015.52 304 | EM_FORE_2015_2781, 2015.78 305 | IPDPFHGINSP_GUI_2015_6505, 2015.33 306 | EM_COY_2015_017091, 2015.40 307 | 0109_C2_020380_EMLK, 2015.65 308 | Makona-UK3, 2015.19 309 | V517, 2014.56 310 | 2208_C2_18642R_EMLH, 2015.51 311 | 0507_C2_MK0392, 2014.97 312 | KG91, 2015.47 313 | KG90, 2015.46 314 | EM_FORE_2015_934, 2015.47 315 | 2607_C2_12916_EMLH, 2015.32 316 | REDC_GUI_2015_01285, 2015.64 317 | EM_COY_2015_016800, 2015.38 318 | EM_079750, 2014.38 319 | 1805_C1_MK2397, 2015.15 320 | 1807_C2_14782_EMLK, 2015.31 321 | G3809, 2014.45 322 | 1805_C1_MK2825, 2015.18 323 | EM_004422, 2015.00 324 | Kissidougou-C15, 2014.21 325 | EM_079753, 2014.39 326 | 2807_C2_77716_EMLK, 2015.02 327 | 1507_C2_MK0866, 2015.01 328 | 2104_C1_MK2343, 2015.15 329 | 1507_C2_MK0864, 2015.01 330 | 0305_C1_PL5201, 2015.22 331 | Gueckedou-C05, 2014.21 332 | EM098, 2014.40 333 | Gueckedou-C07, 2014.21 334 | 1807_C1_15360_EMLK, 2015.43 335 | EM_COY_2015_016278, 2015.34 336 | G3799, 2014.45 337 | CON-10786, 2015.62 338 | V20143360, 2014.83 339 | KG35, 2015.43 340 | J0003, 2014.74 341 | EM120, 2014.42 342 | 1007_C2_MK0020, 2014.93 343 | 1105_C1_MK2790, 2015.18 344 | 1807_C1_PL9150Rb, 2015.53 345 | EM_079442, 2014.25 346 | CON-11010, 2015.64 347 | EM_079444, 2014.25 348 | EM_079659, 2014.34 349 | EM_079731, 2014.38 350 | IPDPFHGINSP_GUI_2015_7070, 2015.38 351 | G3707, 2014.41 352 | V20141643, 2014.76 353 | 2906_C2_MK0366, 2014.97 354 | 2906_C2_MK0368, 2014.97 355 | DML25083, 2015.13 356 | EM_COY_2015_016263, 2015.34 357 | V1116, 2014.73 358 | EM_004085, 2014.96 359 | 0205_C2_PL5950, 2015.27 360 | EM_078639, 2014.92 361 | J0096, 2014.82 362 | LIBR0157, 2014.87 363 | EM_079622, 2014.32 364 | -------------------------------------------------------------------------------- /data/ebola/ebola.nwk: -------------------------------------------------------------------------------- 1 | ((((G3734:0.000000005,((LIBR0605:0.000478047,EM098:0.000000005)1.000:0.000000005,(((LIBR10237:0.000000005,LIBR1221:0.000212455)0.998:0.000000006,(((LIBR10196:0.000000005,(LIBR0622:0.000000005,LIBR0624:0.000000005)1.000:0.000477796)0.832:0.000053082,(LIBR0093:0.000318703,(LIBR0073:0.000267977,(LIBR10217:0.000372989,LIBR10270:0.000212529)0.857:0.000106227)0.872:0.000000005)0.947:0.000000005)0.929:0.000106122,(LIBR10180:0.000000005,((LIBR10056:0.000141891,(LIBR0090:0.000510929,LIBR10053:0.000107802)0.886:0.000107768)0.763:0.000070867,LIBR10017:0.000159902)1.000:0.000000005)0.849:0.000053093)0.000:0.000000005)0.986:0.000000006,Makona-G4437.1:0.000279340)0.000:0.000000005)0.995:0.000000005)1.000:0.000000005,EM120:0.000052896)0.996:0.000000005,G3799:0.000052797)0.911:0.000000005,(((((Makona-G3972.1:0.000000005,EM096:0.000105647)0.793:0.000000005,((G3769:0.000105720,(LIBR10202:0.000159481,(LIBR10077:0.000053256,LIBR0157:0.000106196)0.966:0.000212415)1.000:0.000000005)0.916:0.000000005,G3820:0.000000005)0.723:0.000000005)0.997:0.000000005,(EM_000219:0.000158625,LIBR10205:0.000266449)0.951:0.000211507)1.000:0.000000006,G3782:0.000000005)0.895:0.000000005,G3682:0.000000005)0.000:0.000000005,((G3670:0.000105685,G3823:0.000052783)0.365:0.000000005,(((((EM_000218:0.000105521,(EM_079388:0.000270849,EM_076322:0.000159043)0.928:0.000000005)0.999:0.000000005,(EM_000501:0.000052743,((EM_076610:0.000000005,((NZG_0393:0.000000005,(NZG_0422:0.000000005,NZG_0358:0.000000005)0.781:0.000000005)0.840:0.000056214,((EM_NG_2016_029366:0.0,EM_NG_2016_029364:0.0):0.000000005,(EM_NG_2016_029417:0.000000005,NZG_0381:0.000000005)1.000:0.000000005)0.915:0.000000005)0.987:0.000281308)0.964:0.000211773,(EM_078608:0.000158688,EM_076534:0.000158679)0.883:0.000105728)0.999:0.000000005)0.916:0.000052769)0.844:0.000052732,((LIBR10271:0.000106227,(((EM_000934:0.000317182,EM_074461:0.000052815)0.886:0.000105654,(EM_080213:0.000158292,G3686:0.000000006)0.783:0.000052764)0.826:0.000052738,((G3676:0.000000005,EM095:0.000000005)0.998:0.000000005,(EM_080253:0.000105520,(EM_079410:0.000000006,(Kissidougou-C15:0.000000005,(((((((EM_079412:0.000211011,(EM_079587:0.000000005,(EM_079514:0.000105797,EM_079578:0.000105483)0.736:0.000000005)0.986:0.000316696)0.929:0.000000005,(EM_079444:0.000000005,(EM_079405:0.000000005,(EM_079630:0.000105553,((EM_079659:0.000105573,EM_079622:0.000000005)0.899:0.000105580,((EM_079749:0.000029886,(EM_079681:0.000105667,EM_079753:0.000000005)0.748:0.000029829)0.918:0.000098592,(EM_079685:0.000000005,(EM_079731:0.000000005,EM_079702:0.000105475)0.784:0.000000005)0.215:0.000000005)0.429:0.000052757)0.826:0.000000005)0.844:0.000052757)0.836:0.000000005)0.715:0.000000005)0.733:0.000000005,(EM_079408:0.000000006,(EM_079464:0.000086844,((EM_COY_2015_016449:0.000000005,EM_COY_2015_017018:0.000112527)0.943:0.000168779,((EM_COY_2015_014100:0.000000005,(IPDPFHGINSP_GUI_2015_5117:0.000000005,(IPDPFHGINSP_GUI_2015_4909:0.000056381,((KG12:0.000000005,EM_COY_2015_017091:0.000000005)0.880:0.000112498,(KG90:0.000000005,(KG91:0.000000005,(EM_COY_2015_017574:0.000059372,KG35:0.000000005)0.998:0.000000005)0.522:0.000034162)0.567:0.000022074)0.945:0.000168657)0.495:0.000000005)0.758:0.000000005)0.983:0.000224988,(CON12930:0.000450425,(IPDPFHGINSP_GUI_2015_6505:0.000112529,(EM_COY_2015_016263:0.000232424,(EM_COY_2015_015982:0.000000005,(EM_COY_2015_016642:0.000169003,IPDPFHGINSP_GUI_2015_7070:0.000000005)0.935:0.000112498)0.782:0.000056217)0.764:0.000056239)0.970:0.000225001)0.053:0.000000005)0.757:0.000056213)1.000:0.000618582)0.293:0.000018876)0.840:0.000052841)0.945:0.000105457,(EM_079542:0.000158345,(Gueckedou-C05:0.000052761,(EM_079549:0.000000005,EM_079517:0.000052844)1.000:0.000000006)0.617:0.000000005)0.917:0.000105550)0.664:0.000000005,(Gueckedou-C07:0.000000005,(EM_079421:0.000052778,((((EM_079429:0.000211240,EM_079424:0.000158591)0.746:0.000028264,EM_079434:0.000207917)0.746:0.000027895,EM_079423:0.000000005)0.964:0.000000005,EM_079422:0.000052756)0.841:0.000052780)0.510:0.000000005)0.909:0.000052738)0.649:0.000000005,((EM_079775:0.000000006,((EM_079914:0.000105531,(EM_079815:0.000052771,EM_079750:0.000105549)0.975:0.000000005)0.079:0.000052734,V517:0.000158291)0.336:0.000000006)0.938:0.000158214,(EM_079497:0.000052788,(EM_079413:0.000000005,EM_079414:0.000000005)0.884:0.000105472)0.771:0.000052756)0.888:0.000105465)0.909:0.000105470,EM_079442:0.000052740)0.062:0.000000005)0.859:0.000052770)0.909:0.000052744)0.918:0.000000005)0.925:0.000000005)0.980:0.000211097)0.914:0.000000005,(((LIBR10035:0.000053036,((LIBR0177:0.000371483,LIBR0505:0.000252289)0.921:0.000000005,LIBR10110:0.000000005)0.055:0.000000005)1.000:0.000000005,((EM_076403:0.000000005,(EM_004437:0.000052760,(EM_004422:0.000052970,(EM_004085:0.000000005,EM_004059:0.000106001)0.478:0.000000005)1.000:0.000000005)0.817:0.000052749)0.963:0.000158261,(((EM_078556:0.000158964,EM_078639:0.000369895)0.749:0.000052828,((V633:0.000000005,V1561:0.000106126)0.966:0.000158705,V768:0.000000005)0.741:0.000000005)1.000:0.000000005,EM_074548:0.000000005)0.973:0.000000005)0.937:0.000105543)0.909:0.000105468,(((V20140729:0.000317214,V653:0.000000005)0.900:0.000105484,((G3814:0.000000005,G3827:0.000052993)0.336:0.000000005,((G3809:0.000053123,Makona-G5059.1:0.000269964)1.000:0.000000005,((((J0042:0.000052982,J0134:0.000052982)0.920:0.000000005,(J0112:0.000318135,J0016:0.000105957)0.943:0.000000005)1.000:0.000000005,(((0807_C1_PL4119:0.000106824,(1507_C2_MK0866:0.000000005,(0507_C1_PL4283:0.000000005,(0807_C1_PL4813:0.000106777,(2605_C2_PL5534:0.000000005,0205_C2_PL5950:0.000000006)0.861:0.000053036)0.975:0.000000005)0.951:0.000106007)0.718:0.000052978)1.000:0.000795441,2507_C2_10212_EMLK:0.000318313)1.000:0.000000005,(DML24573:0.000158885,DML25083:0.000106247)0.994:0.000423732)0.981:0.000000005)0.805:0.000000005,(2607_C1_592_EMLH:0.000000005,2807_C2_567_EMLH:0.000000005)1.000:0.000636006)0.958:0.000158787)0.955:0.000000005)0.998:0.000000005)0.690:0.000000005,((((((((J0168:0.000318220,J0003:0.000106858)0.870:0.000106052,(V1039:0.000158742,(Makona-G5853.1:0.000000005,Makona-G5985.1:0.000163959)1.000:0.000000005)0.997:0.000000005)0.957:0.000158335,((V509:0.000000005,(Makona-G3889.1:0.000000005,(Makona-G4423.1:0.000052845,(Makona-G4347.1:0.000000005,Makona-G4264.1:0.000000005)0.730:0.000000005)0.992:0.000000005)1.000:0.000000005)0.000:0.000000005,(((((2807_C2_77716_EMLK:0.000106832,(0208_C1_77679_EMLK:0.000052985,(((1807_C2_14830_EMLK:0.000105885,(1807_C2_14782_EMLK:0.000000005,1807_C1_14888_EMLK:0.000000005)1.000:0.000000005)0.961:0.000158981,(2507_C2_10080_EMLK:0.000052979,(0205_C2_PL5868:0.000000005,0205_C2_PL6086:0.000054299)1.000:0.000000005)0.992:0.000000005)0.925:0.000052981,(2507_C1_77748_EMLK:0.000000005,2807_C2_77693_EMLK:0.000000005)1.000:0.000000005)0.794:0.000052982)0.754:0.000052953)0.988:0.000317983,((1007_C2_PL4105:0.000053439,(3004_C1_KT5974:0.000000005,2906_C2_KT5034:0.000106107)0.784:0.000052997)0.964:0.000212182,(J0129:0.000053166,(((0305_C2_PL4570:0.000052977,(3004_C2_KT5382:0.000000005,(1807_C2_10398_EMLK:0.000000005,(DML12120:0.000106085,2607_C2_12781_EMLH:0.000053009)0.983:0.000000005)0.931:0.000052973)0.263:0.000000005)1.000:0.000000005,((((1805_C1_MK2724:0.000000005,1805_C1_MK2382:0.000000005)0.848:0.000052963,1805_C1_MK2825:0.000052962)0.870:0.000000005,(2507_C2_10353_EMLK:0.000052972,3004_C1_KT5858:0.000105946)0.975:0.000000005)1.000:0.000000005,(2104_C1_MK2343:0.000052970,(1805_C1_MK2397:0.000106789,(1805_C1_MK2255:0.000053394,(Makona-UK3:0.000000005,1105_C1_MK2790:0.000000005)0.922:0.000159269)0.040:0.000000005)0.943:0.000000005)0.832:0.000000005)0.846:0.000052884)0.965:0.000158786,(2507_C1_77795_EMLK:0.000000005,(2507_C2_10084_EMLK:0.000000005,2807_C2_77712_EMLK:0.000000005)0.821:0.000000005)1.000:0.000000005)0.787:0.000052928)0.925:0.000158772)0.738:0.000000005)0.955:0.000000005,(J0124:0.000212103,(J0167:0.000160492,(DML25411:0.000406452,(0806_C1_KT4677:0.000242391,0806_C2_KT4631:0.000000005)0.941:0.000269348)0.972:0.000336657)0.565:0.000000005)0.893:0.000000005)0.988:0.000000005,(J0081:0.000106042,(((J0170:0.000214016,2507_C2_10123_EMLK:0.000160226)1.000:0.000000006,Makona-G5114.1:0.000000005)1.000:0.000000005,Makona-G5112.1:0.000000005)0.780:0.000052848)0.944:0.000158318)0.846:0.000052767,(((EM_080265:0.000158567,J0021:0.000052978)0.753:0.000000005,((((1708_C1_MK0491R:0.000052967,(2906_C2_MK0366:0.000159024,0507_C2_MK0392:0.000212198)0.763:0.000000005)0.927:0.000158905,(V20144192:0.000052871,(2906_C2_MK0368:0.000213352,(0507_C2_MK0664:0.000053341,1507_C2_MK0575:0.000106027)0.801:0.000105992)0.934:0.000000006)0.933:0.000158501)0.755:0.000052820,((J0019:0.0,J0015:0.0):0.000000005,(J0020:0.000106055,J0096:0.000320642)0.946:0.000000005)1.000:0.000000005)0.934:0.000052771,(1007_C2_MK1000:0.000477264,(0806_C1_KT4715:0.000055570,J0123:0.000424222)0.801:0.000000005)0.998:0.000000005)0.782:0.000052766)0.000:0.000000005,((EM_GUI_2015_004674:0.000000005,0205_C2_PL6070:0.000546963)0.972:0.000267457,(EM_COY_2015_015972:0.000225149,((EM_COY_2015_015815:0.000290006,((EM_COY_2015_017135:0.000000005,((CON-10512:0.000056248,(((CON-11010:0.000000005,REDC_GUI_2015_01165:0.000179255)0.834:0.000112497,(REDC_GUI_2015_01323:0.000091505,((FCH_729:0.000134639,(FCH1785_S:0.000000005,(FCH_731:0.000239289,(FCH_730:0.000000005,(EM_FORE_2015_2878:0.000056252,(EM_FORE_2015_2781:0.000000005,REDC_GUI_2015_02242:0.000056243)0.394:0.000000005)0.892:0.000056208)0.917:0.000056243)0.498:0.000000006)0.532:0.000000005)0.750:0.000082017,REDC_GUI_2015_01408:0.000086698)0.294:0.000056208)0.809:0.000082084)0.954:0.000000006,(CON-10590:0.000000005,CON-10193:0.000000005)1.000:0.000000005)0.876:0.000000005)0.850:0.000056243,((EM_COY_2015_016800:0.000000005,(IPDPFHGINSP_GUI_2015_5038:0.000000005,(EM_COY_2015_023747:0.000000005,REDC_GUI_2015_01285:0.000168743)0.891:0.000112488)0.788:0.000000005)0.000:0.000000006,((REDC-GUI-2015-00502:0.000112534,EM_COY_2015_016456:0.000116096)0.987:0.000000005,((EM_COY_2015_016617:0.000000005,EM_COY_2015_016531:0.000000006)0.984:0.000281265,EM_COY_2015_017787:0.000056412)0.737:0.000000005)0.000:0.000000005)0.922:0.000000005)0.749:0.000000005)0.758:0.000067502,A023888:0.000134140)0.964:0.000269915)0.754:0.000056209,(((EM_COY_2015_015980:0.000281199,CON-8559:0.000563386)0.871:0.000112443,(1807_C2_14795_EMLK:0.000105992,(0807_C1_14750_EMLK:0.000212170,0205_C1_PL5428:0.000216000)0.783:0.000053028)0.740:0.000000005)0.000:0.000000005,(EM_COY_2015_016278:0.000000005,(EM_FORE_2015_697:0.000112809,((EM_FORE_2015_1023:0.000000005,(EM_FORE_2015_934:0.000286679,REDC-GUI-2015-00497:0.000000005)0.991:0.000000005)0.922:0.000000005,(((EM_FORE_2015_1313:0.000056278,EM_FORE_2015_1437:0.000056214)0.386:0.000000005,(EM-FORE-2015-664:0.000056188,EM_COY_2015_017174:0.000000005)0.650:0.000000043)0.690:0.000000005,(((EM_FORE_2015_1076:0.000000005,EM_FORE_2015-1971:0.000225043)0.748:0.000000005,(EM_COY_2015_022059:0.000000005,EM_FORE_2015_1140:0.000000006)1.000:0.000000005)0.134:0.000000005,(CON-8811:0.0,EM-FORE-2015-1414:0.0,CON-10786:0.0):0.000000005)0.000:0.000000005)1.000:0.000000006)0.831:0.000000005)0.921:0.000112491)0.958:0.000168745)0.444:0.000000005)0.232:0.000000005)0.074:0.000000006)0.985:0.000318128)0.394:0.000000005)0.217:0.000000005)0.000:0.000000005)0.458:0.000000005,((Makona-G5982.1:0.000158601,0106_C2_KT2316:0.000689638)0.543:0.000000005,(((2507_C1_77767_EMLK:0.000477531,3007_C2_77581_EMLK:0.000320363)1.000:0.000000005,Makona-G4972.1:0.000000005)0.989:0.000000005,(V20143036:0.000158482,(2507_C1_10022_EMLK:0.000213476,(0305_C1_PL5201:0.000052967,(0807_C1_PL4123:0.000000005,2208_C1_PL4256R:0.000000005)1.000:0.000000005)0.764:0.000052967)0.771:0.000053001)0.875:0.000105649)0.837:0.000052824)0.858:0.000052809)0.748:0.000000005,(V20146578:0.000289094,((J0037:0.000265972,((J0056:0.000320668,((V20144820:0.000106500,(V20143415:0.000000005,V20143360:0.000000005)0.944:0.000158338)0.859:0.000105563,(1708_C1_12705_EMLH:0.000583772,J0161:0.000000005)1.000:0.000000005)0.770:0.000052760)0.909:0.000105522,(J0076:0.000052989,J0127:0.000371270)0.762:0.000053016)0.760:0.000052736)0.790:0.000052763,((V20140024:0.000000005,3004_C2_KT5320:0.000265307)0.818:0.000052829,((1309_C2_MK13013:0.000530731,1007_C2_MK0020:0.000052984)0.967:0.000212064,((1708_C2_MK2656R2:0.000267094,V20143648:0.000106337)0.962:0.000212601,1507_C2_MK0864:0.000159189)1.000:0.000000005)1.000:0.000000006)1.000:0.000000005)0.580:0.000059828)0.574:0.000045652)0.827:0.000000005,V1116:0.000263829)0.844:0.000052749,(((((Makona-G4942.1:0.000052992,Makona-G4312.2:0.000000005)0.854:0.000052899,(Makona-G4422.1:0.000053109,Makona-G4702.1:0.000053049)1.000:0.000000006)0.904:0.000000005,(Makona-G4415.1:0.000423523,(J0169:0.000052795,(2607_C2_12916_EMLH:0.000000005,(2607_C2_12855_EMLH:0.000000005,(1708_C1_13031_EMLH:0.000053165,((((1507_C1_13268_EMLH:0.000107127,(1507_C1_18647_EMLH:0.000000005,(0208_C1_MK10173:0.000052990,(1507_C1_18706_EMLH:0.000049037,2208_C2_18659R_EMLH:0.000159266)0.632:0.000001584)0.000:0.000000663)0.011:0.000001021)0.674:0.000001366,1507_C1_18650_EMLH:0.000053022)0.642:0.000001060,(2208_C2_18642R_EMLH:0.000000005,(1507_C1_18636_EMLH:0.000053042,2208_C2_18687R_EMLH:0.000053039)0.970:0.000000005)0.929:0.000105933)0.288:0.000000005,1507_C1_18660_EMLH:0.000106739)0.986:0.000273808)0.778:0.000054751)0.462:0.000000005)0.999:0.000547967)1.000:0.000711596)0.896:0.000210939)0.124:0.000008567,LIBR0430:0.000376730)0.611:0.000044190,(G3707:0.000000005,((2906_C1_PL4483:0.000106811,((0205_C2_PL6049:0.000159043,((2208_C2_15207R_EMLK:0.000000005,(1807_C1_15421_EMLK:0.000000005,((0809_C1_020484_EMLK_A:0.000000005,((1209_C1_20573_EMLK:0.000053209,1009_C1_20524_EMLK:0.000000005)1.000:0.000000005,(0109_C2_020380_EMLK:0.000000005,1009_C1_20547_EMLK:0.000000005)0.861:0.000000006)0.427:0.000000005)0.961:0.000159041,(0809_C1_19560_EMLK_E:0.000000005,1009_C1_20525_EMLK:0.000000005)1.000:0.000000006)0.924:0.000052968)0.917:0.000052967)0.995:0.000318063,1807_C2_14763_EMLK:0.000105958)0.772:0.000052998)0.912:0.000000005,((1706_C1_PL7801:0.000108846,(0806_C1_PL7376:0.000000005,((1807_C1_15360_EMLK:0.000052964,(1507_C2_15674_EMLK:0.000105976,2906_C1_PL8172:0.000053017)0.382:0.000000005)0.443:0.000000005,(((1807_C1_15327_EMLK:0.000000005,1807_C1_PL8310b:0.000053048)1.000:0.000000005,(1807_C1_PL9150R:0.000052997,(1807_C1_PL9150Rb:0.000000005,(Combined_PL9192:0.000055156,1807_C1_PL9199Rb:0.000000005)1.000:0.000000005)0.450:0.000000005)0.857:0.000052993)0.936:0.000105990,1807_C2_14846_EMLK:0.000106029)0.859:0.000000005)0.960:0.000000005)0.722:0.000043162)0.873:0.000009767,(0106_C2_PL7375:0.000108592,1706_C1_PL7709:0.000000005)0.888:0.000054252)1.000:0.000000038)0.745:0.000052968)0.981:0.000264966,(J0053:0.000052981,J0137:0.000212128)1.000:0.000000005)0.958:0.000158612)0.000:0.000000005)0.737:0.000000005)0.938:0.000000005,((((Makona-G4252.1:0.000052868,(((NM042:0.000000005,Makona-G4250.1:0.000000005)0.870:0.000000005,(EM111:0.0,EM110:0.0):0.000000005)0.955:0.000000005,Makona-G4236.1:0.000000005)0.000:0.000000005)0.000:0.000000005,(Makona-G4419.1:0.000105737,V20141643:0.000211466)0.749:0.000052837)0.805:0.000000005,Makona-G3917.1:0.000000005)1.000:0.000000005,(G3770:0.000105456,(G3735:0.000000005,((Makona-G4416.1:0.000105554,V1211:0.000211376)0.782:0.000052746,(Makona-G4348.1:0.000105674,G3840:0.000000005)0.564:0.000000005)0.956:0.000000005)0.910:0.000000005)0.000:0.000000005)0.189:0.000000005)0.882:0.000000005)0.845:0.000052767)0.893:0.000000005)0.910:0.000000005)0.922:0.000000005,G3677:0.000000005)0.948:0.000000005,((EM_076948:0.000316973,(EM_004192:0.000052832,EM_004555:0.000158682)0.481:0.000000005)0.990:0.000000005,EM_000921:0.000158269)0.957:0.000158350)0.846:0.000000005)0.925:0.000000006); 2 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_20.fasta: -------------------------------------------------------------------------------- 1 | >A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409 2 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 3 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 4 | GAATTCGACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 5 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 6 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTTC 7 | TCTAAGGACAATTCAATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 8 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 9 | AACAACGTGCATTCAAATAACACAGTACGTRATAGGACCCCTTATCGGACTCTATTGATG 10 | AATGAGTTGGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 11 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 12 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 13 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 14 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 15 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTTGAAGAGTGCTCTTGC 16 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATCGG 17 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 18 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 19 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTCGATGATGGAAATGACGTG 20 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 21 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 22 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 23 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 24 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 25 | GGGGCGGACCTCAACCTCATGCCTATA 26 | >A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409 27 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 28 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 29 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 30 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 31 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTTC 32 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 33 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 34 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTCTATTGATG 35 | AATGAGTTGGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 36 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGCATAACGGGGGATGATAAAAAT 37 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 38 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 39 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGA 40 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGC 41 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATCGG 42 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 43 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 44 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 45 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 46 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 47 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 48 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 49 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 50 | GGGGCGGACCTCAATCTCATGCCTATA 51 | >A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409 52 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 53 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 54 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 55 | AATATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 56 | CTAGCAGAGTACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGGTTTGCACCTTTT 57 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 58 | TATGTGTCATGCGACCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 59 | AACAACGTACATTCAAATAACACAGTACGTGRTAGGACCCCTTATCGGACCCTATTGATG 60 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 61 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 62 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 63 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 64 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 65 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGC 66 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGATCCAATAGG 67 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTCTCCAGTTATGTGTGTTCAGGA 68 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 69 | AACAATGAGGAAGGTGGTCATGGGGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 70 | TGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 71 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 72 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 73 | TGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 74 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 75 | GGGGCGGACATCAATCTCATGCCTATA 76 | >A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416 77 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 78 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 79 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 80 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 81 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGGTTTGCACCTTTT 82 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 83 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 84 | AACAACGTACATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATG 85 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 86 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 87 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 88 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 89 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATATTATTCATTGAGGAGGGA 90 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGC 91 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGATCCAATAGG 92 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTCTCCAGTTATGTGTGTTCAGGA 93 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 94 | AACAATGAGGAAGGTGGTCATGGGGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 95 | TGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 96 | GAAGGCTGGTCCAACCCTAAGTCCAAACTGCAGATAAATAGGCAAGTCATAGTTGACAGA 97 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 98 | TGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 99 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 100 | GGGGCGGACATCAATCTCATGTCTGTA 101 | >A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409 102 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTGCCACAATA 103 | TGCTTCCTTATGCAAATTGCCATCCTGGTAACTACTGTAACATTGCATTTCAAGCAATAT 104 | GAATGCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 105 | AACATAACAGAGATAGTATATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 106 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTT 107 | TCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 108 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 109 | AACAACGGGCATTCAAATGACACAGTACATGATAGGACCCCTTATCGAACCCTATTGATG 110 | AATGAGTTGGGTGTTCCATTTCATTTGGGAACCAAGCAAGTGTGCATAGCATGGTCCAGC 111 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTGTAACGGGGGATGATGAAAAT 112 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGGTTCATGGTCCAAA 113 | AAAATCCTCAGGACCCAGGAGTCGGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 114 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 115 | AAAATCGTTCATACTAGCTCATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGT 116 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 117 | CCCATCGTAGATATAAATGTAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGA 118 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGCTTGGATCCT 119 | AACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 120 | TGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAGGATATGAAACCTTCAAAGTCATT 121 | GAAGGCTGGTCCAAACCTAACTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 122 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 123 | TGCTTTTATGTGGAGTTGATAAGGGGAAGGAAACAGGAAACTGAAGTCTTGTGGACCTCA 124 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 125 | GGGGCGGACATCAATCTCATGCCTATA 126 | >A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416 127 | ATGAATCCAAATCAAAAGATAATAACGATTGGTTCTGTTTCTCTCACCATTGCCACAATA 128 | TGCTTCCTTATGCAAGTTGCCATCCTGGTAACTACTGTAACATTGCATTTCAAGCAATAT 129 | GAATGCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 130 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 131 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTT 132 | TCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 133 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 134 | AACAACGGGCATTCAAATGACACAGTACATGATAGGACCCCTTATCGGACCCTATTGATG 135 | AATGAGTTGGGTGTTCCATTTCATTTGGGAACCAAGCAAGTGTGCATAGCATGGTCCAGC 136 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTGTAACGGGGGATGATGAAAAT 137 | GCAACTGCCAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGGTTCATGGTCCAAA 138 | AAAATCCTCAGGACCCAGGAGTCGGAATGCGTTTGTATCAATGGAACTTGTACAGTGGTA 139 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 140 | AAAATCGTTCATACTAGCCTATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGT 141 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 142 | CCCATCGTAGATATAAATGTAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGA 143 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGCTTGGATCCT 144 | AACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGATGTG 145 | TGGATGGGAAGAACAATCAGCGAGAAGTTACGCTCAGGATATGAAACCTTCAAAGTCATT 146 | GAAGGCTGGTCCAAACCTAACTCCAAACTGCAGATAAATAGGCAAGTCATAGTTGACAGA 147 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 148 | TGCTTTTATGTGGAGTTGATAAGGGGAAGGAAACAGGAAACTGAAGTTTTGTGGACCTCA 149 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 150 | GGGGCGGACATCAATCTCATGCCTATA 151 | >A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428 152 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 153 | TGCTTCTTCATGCAAATTGCCATCTTGATGACTACTGTAACATTGCATTTCAAGCAATGT 154 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 155 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 156 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTT 157 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 158 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 159 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATG 160 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATGGCATGGTCCAGC 161 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGAATGATAAAAAT 162 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 163 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 164 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATATTATTCATTGAGGAGGGG 165 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGC 166 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGATCCAATAGG 167 | CCCATTGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTATGTTCAGGA 168 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 169 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 170 | TGGATGGGAAGAACGATCACCGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 171 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 172 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 173 | TGCTTTTATGTGGAATTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 174 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 175 | GGGGCGGACATCAATCTCATGCCTATA 176 | >A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409 177 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 178 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACCGTAACATTGCATTTCAAGCAATAT 179 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 180 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 181 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGACATTACAGGATTTGCACCTTTT 182 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 183 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 184 | AACAATGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTTTATTGATG 185 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 186 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 187 | GCAACTGCTAGCTTCATTTACAATGGGAAGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 188 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 189 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 190 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGC 191 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 192 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTCTCCAGTTATGTGTGTTCAGGA 193 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 194 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 195 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 196 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 197 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 198 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 199 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 200 | GGGGCGGACCTCAATCTCATGCCTATA 201 | >A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409 202 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 203 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 204 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 205 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 206 | CCAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGGCATTACAGGATTTGCACCTTTC 207 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 208 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 209 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTCTATTGATG 210 | AATGAGTTGGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 211 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 212 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 213 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 214 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 215 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGC 216 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATCGG 217 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 218 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 219 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 220 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 221 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 222 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 223 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 224 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 225 | GGGGCGGACCTCAATCTCATGCCTATA 226 | >A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409 227 | ATGAATCCAAATCAAAAGATAATAACAATTGGCTCTGTTTCTCTCACCATTGCCGCAATA 228 | TGCTTCCTTATGCAAATTGCCATCCTGGTAACCACTGTAACATTGCATTTCAAGCAGCAT 229 | GAATGCAACTCCCCCCCAAACAACCAAGTAATGCTGTGTGAACCAACAATAATAGAAAGA 230 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 231 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTT 232 | TCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 233 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGGCAGGGAACAACACTA 234 | AACAACGGGCATTCAAATGACACAGTACATGATAGGACCCCTTACCGGACCCTATTGATG 235 | AATGAATTGGGTGTTCCATTTCATTTGGGAACCAGGCAAGTGTGCATAGCATGGTCCAGC 236 | TCAAGTTGTCACGATGGAAAAGCGTGGCTGCATGTTTGTGTAACTGGGGATGATAAAAAT 237 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGGTTCATGGTCCAAA 238 | AAAATACTCAGAACCCAGGAGTCGGAATGCGTTTGTATCAATGGAACTTGTACAGTGGTA 239 | ATGACTGATGGAAGCGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 240 | AAAATCGTTCATATTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGT 241 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 242 | CCCATTGTAGATATAAATGTAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGA 243 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTTCAGCAGTAGCCATTGCCTAGATCCT 244 | AACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 245 | TGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAGGTTATGAAACCTTCAAAGTCATC 246 | GAAGGCTGGTCCAAACCTAACTCCAAATTACAGATAAATAGGCAAGTTATAGTTGAAAGA 247 | GGTAACAGGTCCGGTTATTCTGGTATTTTCTCCGTTGAAGGCAAAAGCTGCATCAATCGG 248 | TGCTTTTATGTGGAGTTGATAAGGGGAAGGAAAGAGGAAACTGAAGTCTGGTGGACCTCA 249 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 250 | GGGGCGGATATCAATCTCATGCCTATA 251 | >A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409 252 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 253 | TGCTTCTTCATGCAAATTGCCATCTTGGCAACTACTGTAACATTGCATTTCAAGCAATAT 254 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 255 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 256 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTT 257 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 258 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 259 | AACAACGTGCATTCAAATGACACAGTACGTGGTAGGACCCCTTATCGGACCCTATTGATG 260 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 261 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 262 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAA 263 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 264 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 265 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGC 266 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 267 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 268 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 269 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 270 | TGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 271 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAAA 272 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 273 | TGCTTTTATGTAGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 274 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 275 | GGGGCGGACATCAATCTCATGCCTATA 276 | >A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409 277 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 278 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 279 | GAATTCAACTCCTCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 280 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 281 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTT 282 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 283 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 284 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATG 285 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTCTGCATAGCATGGTCCAGC 286 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 287 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAA 288 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 289 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 290 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGC 291 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 292 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 293 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 294 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 295 | TGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 296 | GAAGGCTGGTCCAATCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 297 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 298 | TGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 299 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 300 | GGGGCGGACATCAATCTCATGCCTATA 301 | >A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412 302 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 303 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 304 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 305 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 306 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTT 307 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 308 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 309 | AACAACGTGCATTCAAATGACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATG 310 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 311 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 312 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAA 313 | GAAATCCTCAGGACCCAGGAGTCAGAATGTGTTTGTATCAATGGAACTTGTACAGTAGTA 314 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 315 | AAGATCGTTCATACTAGCACATTGTCAGGAAGTGCTAAGCATGTTGAGGAGTGCTCCTGC 316 | TATCCTCGACATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 317 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 318 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 319 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 320 | TGGATGGGAAGAACGATCAGCGAGAAGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 321 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 322 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 323 | TGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 324 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 325 | GGTGCGGACATCAATCTCATGCCTATA 326 | >A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423 327 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCCCTCACCATTTCCACAATA 328 | TGCTTCTTCATGCAAATTGCCATCCTGATAACTACTGTAACATTGCATTTCAAGCAATAT 329 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 330 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 331 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTT 332 | TCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 333 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGAMAGGGAACAACACTA 334 | AACAACGTGCATTCAAATGACACAGTACATGATAGGACCCCTTATCGGACCCTATTGATG 335 | AATGAGTTGGGTGTTCCATTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCAAGC 336 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTGTAACGGGGGATGATGAAAAT 337 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGTTTCATGGTCCAAA 338 | AAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 339 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 340 | AAAATTGTTCATACTAGCACATTATCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGT 341 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 342 | CCCATCGTAGATATAAACATAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGA 343 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGCTTGGATCCA 344 | AACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 345 | TGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAGGATATGAAACCTTCAAAGTCATT 346 | GAAGGCTGGTCCAACCCTAACTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 347 | GGTAACAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAGGGCAAAAGCTGCATCAATCGG 348 | TGCTTTTATGTGGAGTTGATAAGGGGAAGAAAACAGGAAACTGAAGTCTTGTGGACCTCA 349 | AACAGTATTGTTGTGTTTTGTGGCACATCAGGTACATATGGAACAGGCTCATGGCCTGAT 350 | GGGGCGGACATCAATCTCATGCCTATA 351 | >A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409 352 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 353 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 354 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 355 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 356 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTAC 357 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 358 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 359 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTCTATTGATG 360 | AATGAGTTGGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 361 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 362 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 363 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 364 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 365 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAAGAATGCTCTTGC 366 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 367 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 368 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 369 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 370 | TGGATGGGAAGAACAATCAACGAGACATCACGCTTAGGATATGAAACCTTCAAAGTCATT 371 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 372 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 373 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 374 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 375 | GGGGCGGACCTCAATCTCATGCCTATA 376 | >A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409 377 | ATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATA 378 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 379 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 380 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 381 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGACATTACAGGATTTGCACCTTTT 382 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 383 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 384 | AATAATGTGCATTCGAATAACACAGTACGTRATAGGACCCCTTATCGGACTTTATTGATG 385 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 386 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 387 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 388 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 389 | ATGACTGATGGAAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 390 | AAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGC 391 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 392 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTCTCCAGTTATGTGTGTTCAGGA 393 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 394 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 395 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 396 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 397 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 398 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 399 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 400 | GGGGCGAACCTCAATCTCATGCCTATA 401 | >A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409 402 | ATGAATCCAAATCAAAAGATAATAACAATTGGCTCTGTTTCTCTCACCATTGCCACAATA 403 | TGCTTCCTTATGCAAATTGCCATCCTGGTAACTACTGTAACATTGCATTTCAAGCAGCAT 404 | GAATGCAACTCCCCCCCAAACAACCAAGTAATGCTGTGTGAACCAACAATAATAGAAAGA 405 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 406 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTAACATTACAGGATTTGCACCTTTT 407 | TCTAAGGACAATTCGATTCGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 408 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGGCAGGGAACAACACTA 409 | AACAACGGGCATTCAAATGACACAGTACATGATAGGACCCCTTACCGGACCCTATTGATG 410 | AATGAATTGGGTGTTCCATTTCATTTGGGAACCAGGCAAGTGTGCATAGCATGGTCCAGC 411 | TCAAGTTGTCACGATGGAAAAGCGTGGCTGCATGTTTGTGTAACTGGGGATGATAAAAAT 412 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTATTGGTTCATGGTCCAAA 413 | AAAATACTCAGAACCCAGGAGTCGGAATGCGTTTGTATCAATGGAACTTGTACAGTGGTA 414 | ATGACTGATGGAAGCGCTTCAGGGAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 415 | AAAATCGTTCATATTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCCTGT 416 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 417 | CCCATTGTAGATATAAATGTAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGA 418 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTTCAGCAGTAGCCATTGCCTAGATCCT 419 | AACAATGAGGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 420 | TGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAGGTTATGAAACCTTCAAAGTCATC 421 | GAAGGCTGGTCCAAACCTAACTCCAAATTACAGATAAATAGGCAAGTTATAGTTGAAAGA 422 | GGTAACAGGTCCGGTTATTCTGGTATTTTCTCCGTTGAAGGCAAAAGCTGCATCAATCGG 423 | TGCTTTTATGTGGAGTTGATAAGGGGAAGGAAAGAGGAAACTGAAGTCTGGTGGACCTCA 424 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 425 | GGGGCGGATATCAATCTCATGCCTATA 426 | >A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416 427 | ATGAATCCAAATCAAAAGATAATAACAATTGGCTCTGTTTCTCTCACCATTTCCACAATA 428 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTACATTTCAAGCAATAT 429 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 430 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 431 | CTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTGACATTACAGGATTTGCACCTTTT 432 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 433 | TATGTGTCATGCGATCCTAACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 434 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACCCTATTGATG 435 | AATGAGTTAGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 436 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 437 | GCAACTGCTAGCTTCATTTACAATGGGAAGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 438 | GAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 439 | ATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 440 | AAAATCGTTCATACTAGTACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCTTGC 441 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGG 442 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 443 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 444 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 445 | TGGATGGGAAGAACGATCAACGAGACTTCACGTTTAGGGTATGAAACCTTCAAAGTCATT 446 | GAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 447 | GGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGG 448 | TGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 449 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 450 | GGGGCGGACCTCAATCTCATGCCTATA 451 | >A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409 452 | ATGAATCCAAATCAAAAGATAATAACAATTGGCTCTGTTTCTCTCACCATTTCCACAGTA 453 | TGCTTCTTCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATAT 454 | GAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGA 455 | AACATAACAGAGATAGTGTATCTGACCAACACCACCATAGAGAAGGAAATATGCCCCAAA 456 | CCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTTC 457 | TCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCT 458 | TATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACACTA 459 | AACAACGTGCATTCAAATAACACAGTACGTGATAGGACCCCTTATCGGACTCTATTGATG 460 | AATGAGTTGGGTGTTCCTTTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGC 461 | TCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAAT 462 | GCAACTGCTAGCTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAA 463 | GAAATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTA 464 | ATGACTGATGGAAGTGCTTCAGGAGAAGCTGATACTAAAATACTATTCATTGAGGAGGGG 465 | AAAATCATTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGC 466 | TATCCTCGATATCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATCGG 467 | CCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGA 468 | CTTGTTGGAGACACACCCAGAAAAAACGACAGCTCCAGCAGTAGCCATTGTTTGGATCCT 469 | AACAATGAAGAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTG 470 | TGGATGGGAAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCATT 471 | GAAGGCTGGTCCAATCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGA 472 | GGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAACTGCATCAATCGG 473 | TGCTTTTATGTAGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCA 474 | AACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGAT 475 | GGGGCGGACCTCAATCTCATGCCTATA 476 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_20.metadata.csv: -------------------------------------------------------------------------------- 1 | name, date 2 | A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409,2013.40520192 3 | A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409,2012.83778234 4 | A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409,2009.48186174 5 | A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416,2009.5229295 6 | A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409,2000.13415469 7 | A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416,2000.68172485 8 | A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428,2011.98015058 9 | A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409,2011.95550992 10 | A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409,2012.8569473 11 | A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409,2003.84052019 12 | A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409,2007.48733744 13 | A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409,2008.15058179 14 | A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412,2008.86516085 15 | A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423,2003.00273785 16 | A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409,2012.25735797 17 | A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409,2011.98562628 18 | A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409,2003.00273785 19 | A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416,2011.65160849 20 | A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409,2013.11225188 21 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_20.nex: -------------------------------------------------------------------------------- 1 | #NEXUS 2 | Begin Taxa; 3 | Dimensions NTax=19; 4 | TaxLabels A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409 A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416 A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428 A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409 A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416 A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409 A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412 A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409 A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423 A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409 A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409 A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409 A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416 A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409 A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409 A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409 A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409 A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409 A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409; 5 | End; 6 | Begin Trees; 7 | Tree tree1=((A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409:0.00285,((A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416:0.00517,(A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428:0.00761,((A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409:0.00214,A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416:0.00357)0.98:0.00426,(A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409:0.00214,(A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412:0.00428,(A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409:0.00350,(A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423:0.00578,(A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409:0.00210,((A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409:0.00143,A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409:0.00070)1.00:0.02186,A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416:0.00647)0.73:0.00066)1.00:0.01010)1.00:0.01374)0.87:0.00055)0.80:0.00071)0.81:0.00074)0.81:0.00199)0.79:0.00184)0.98:0.00486,(A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409:0.00142,A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409:0.00214)0.93:0.00214)0.96:0.00286)0.81:0.00071,(A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409:0.00500,A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409:0.00071)0.47:0.00055,(A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409:0.00357,A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409:0.00142)0.45:0.00055):0.00000; 8 | End; 9 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_20.nwk: -------------------------------------------------------------------------------- 1 | ((A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409:0.00285,((A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416:0.00517,(A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428:0.00761,((A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409:0.00214,A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416:0.00357)0.977:0.00426,(A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409:0.00214,(A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412:0.00428,(A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409:0.00350,(A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423:0.00578,(A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409:0.00210,((A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409:0.00143,A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409:0.00070)1.000:0.02186,A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416:0.00647)0.731:0.00066)1.000:0.01010)0.999:0.01374)0.872:0.00055)0.803:0.00071)0.813:0.00074)0.813:0.00199)0.785:0.00184)0.983:0.00486,(A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409:0.00142,A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409:0.00214)0.931:0.00214)0.959:0.00286)0.810:0.00071,(A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409:0.00500,A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409:0.00071)0.472:0.00055,(A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409:0.00357,A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409:0.00142)0.450:0.00055); 2 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_200.metadata.csv: -------------------------------------------------------------------------------- 1 | name, date 2 | A/Texas/UR06_0358/2007|CY027565|02/20/2007|USA|06_07|H3N2/5-1413, 2007.13963039 3 | A/Western_Australia/8/2000|CY015662|10/17/2000|Australia||H3N2/1-1409, 2000.79671458 4 | A/Australia/NHRC0008/2003|CY091279|07/08/2003|Australia||H3N2/4-1412, 2003.5174538 5 | A/Canterbury/404/2003|CY007045|07/05/2003|New_Zealand||H3N2/8-1416, 2003.50924025 6 | A/California/VRDL183/2009|CY068696|04/27/2009|USA|08_09|H3N2/4-1412, 2009.32032854 7 | A/Denmark/120/2003|EU103940|2003|Denmark||H3N2/1-1409, 2003.00273785 8 | A/New_York/407/2002|CY003426|01/08/2002|USA|01_02|H3N2/8-1416, 2002.02190281 9 | A/South_Australia/72/2000|CY021775|2000|Australia||H3N2/1-1409, 2000.00273785 10 | A/South_Carolina/07/2008|GQ385873|12/31/2008|USA|08_09|H3N2/1-1409, 2009.00205339 11 | A/North_Carolina/10/2011|KC892419|12/01/2011|USA|11_12|H3N2/1-1409, 2011.91718001 12 | A/Hong_Kong/CUHK40210/2005|EU857280|06/06/2005|Hong_Kong||H3N2/1-1409, 2005.42984257 13 | A/Bilthoven/628/1976|CY113191|1976|Netherlands||H3N2/4-1412, 1976.00273785 14 | A/Malaysia/1681079/2006|CY118940|11/24/2006|Malaysia||H3N2/4-1412, 2006.89801506 15 | A/Mississippi/01/2013|KF790359|01/08/2013|USA|12_13|H3N2/1-1409, 2013.02190281 16 | A/Novosibirsk/707/2009|CY053673|03/2009|Russia|08_09|H3N2/16-1424, 2009.16427105 17 | A/Boston/DOA2_104/2012|CY148358|12/22/2012|USA|12_13|H3N2/1-1409, 2012.97741273 18 | A/Boston/DOA01/2011|CY111128|01/03/2011|USA|10_11|H3N2/4-1412, 2011.00821355 19 | A/Saint_Petersburg/RII03/2012|CY114550|02/06/2012|Russia|11_12|H3N2/9-1417, 2012.10130048 20 | A/New_South_Wales/21/1999|CY016557|1999|Australia||H3N2/5-1413, 1999.00273785 21 | A/HaNoi/Q638/2007|CY105736|08/29/2007|Viet_Nam||H3N2/4-1412, 2007.65982204 22 | A/Texas/40/2009|GQ895023|02/24/2009|USA|08_09|H3N2/1-1409, 2009.15058179 23 | A/Iowa/14/2012|KF790285|10/18/2012|USA|12_13|H3N2/1-1409, 2012.79945243 24 | A/Boston/DOA24/2011|CY116709|02/01/2011|USA|10_11|H3N2/4-1412, 2011.08761123 25 | A/New_York/UR07_0080/2008|CY036969|02/25/2008|USA|07_08|H3N2/1-1409, 2008.15331964 26 | A/Nanchang/0074/94|CY003754|1994|China||H3N2/8-1416, 1994.00273785 27 | A/Nebraska/02/2013|KF790067|01/02/2013|USA|12_13|H3N2/1-1409, 2013.0054757 28 | A/Peru/PER251/2010|CY162258|10/12/2010|Peru||H3N2/8-1416, 2010.78028747 29 | A/Hong_Kong/CUHK51424/2001|EU857312|12/26/2001|Hong_Kong||H3N2/1-1409, 2001.98562628 30 | A/Kentucky/11/2010|KC883205|10/18/2010|USA|10_11|H3N2/1-1409, 2010.79671458 31 | A/Colorado/07/2011|KC892191|10/23/2011|USA|11_12|H3N2/1-1409, 2011.81040383 32 | A/Cambodia/V1013305/2011|KC118547|10/10/2011|Cambodia||H3N2/1-1409, 2011.77481177 33 | A/Peru/PER389/2012|CY163314|04/02/2012|Peru||H3N2/8-1416, 2012.25462012 34 | A/Port_chalmers/1/1973|CY009350|1973|New_Zealand||H3N2/8-1416, 1973.00273785 35 | A/Kentucky/UR07_0148/2008|CY038857|03/10/2008|USA|07_08|H3N2/1-1409, 2008.19164956 36 | A/Hong_Kong/CUHK71313/2003|EU857364|09/21/2003|Hong_Kong||H3N2/1-1409, 2003.72279261 37 | A/Pennsylvania/04/2007|EU516043|03/03/2007|USA|06_07|H3N2/1-1409, 2007.16974675 38 | A/Singapore/GP1797/2011|CY124274|11/29/2011|Singapore||H3N2/20-1428, 2011.91170431 39 | A/New_York/665/1994|CY011522|12/16/1994|USA|94_95|H3N2/8-1416, 1994.95824778 40 | A/Fujian/445/2003|CY121450|2003|China||H3N2/1-1409, 2003.00273785 41 | A/Hong_Kong/CUHK12794/1997|EU857131|06/11/1997|Hong_Kong||H3N2/1-1409, 1997.44353183 42 | A/Kentucky/UR06_0158/2007|CY026885|02/05/2007|USA|06_07|H3N2/5-1413, 2007.09856263 43 | A/Hong_Kong/H090_763_V2|JN256790|08/03/2009|Hong_Kong||H3N2/1-1409, 2009.58863792 44 | A/Lyon/672/1993|CY113983|02/22/1993|France|92_93|H3N2/4-1412, 1993.14510609 45 | A/Wellington/55/2004|CY020343|09/27/2004|New_Zealand||H3N2/5-1413, 2004.74195756 46 | A/Memphis/3/80|CY008470|1980|USA||H3N2/8-1416, 1980.00273785 47 | A/Singapore/C2011.641/2011|KF014491|08/22/2011|Singapore||H3N2/20-1428, 2011.64065708 48 | A/California/14/2013|KF789566|01/29/2013|USA|12_13|H3N2/1-1409, 2013.07939767 49 | A/Boston/DOA2_158/2013|CY148766|01/03/2013|USA|12_13|H3N2/1-1409, 2013.00821355 50 | A/TayNguyen/TN348/2005|CY105376|08/01/2005|Viet_Nam||H3N2/5-1413, 2005.58316222 51 | A/Singapore/GP1382/2011|CY124208|08/03/2011|Singapore||H3N2/20-1428, 2011.58863792 52 | A/England/460/2003|CY088088|11/11/2003|United_Kingdom|03_04|H3N2/1-1409, 2003.862423 53 | A/Singapore/C2009.515/2009|KF014467|07/07/2009|Singapore||H3N2/20-1428, 2009.51471595 54 | A/New_York/381/2004|CY002250|12/28/2004|USA|04_05|H3N2/18-1426, 2004.99383984 55 | A/Guangdong/460/2010|CY091846|10/22/2010|China||H3N2/20-1428, 2010.80766598 56 | A/Moscow/02/2012|JQ988034|02/01/2012|Russia|11_12|H3N2/22-1430, 2012.08761123 57 | A/Peru/PER388/2011|CY163306|09/14/2011|Peru||H3N2/8-1416, 2011.70362765 58 | A/Singapore/GP1583/2011|CY124238|10/07/2011|Singapore||H3N2/20-1428, 2011.76659822 59 | A/Waikato/51/2002|CY012058|08/12/2002|New_Zealand||H3N2/8-1416, 2002.61327858 60 | A/New_York/320/1999|CY001858|03/26/1999|USA|98_99|H3N2/17-1425, 1999.23271732 61 | A/England/492/2003|CY088288|11/21/2003|United_Kingdom|03_04|H3N2/1-1409, 2003.88980151 62 | A/Denmark/72/2003|EU103942|2003|Denmark||H3N2/1-1409, 2003.00273785 63 | A/New_York/517/1998|CY006285|01/03/1998|USA|97_98|H3N2/4-1412, 1998.00821355 64 | A/Singapore/H2011.507/2011|KF014518|07/04/2011|Singapore||H3N2/20-1428, 2011.5065024 65 | A/Waikato/1/2001|CY011970|04/25/2001|New_Zealand||H3N2/2-1410, 2001.31485284 66 | A/Netherlands/357/1993|CY114071|12/06/1993|Netherlands|93_94|H3N2/4-1412, 1993.93086927 67 | A/Peru/PER395/2011|CY163362|10/24/2011|Peru||H3N2/8-1416, 2011.81314168 68 | A/Boston/DOA2_110/2012|CY148406|12/07/2012|USA|12_13|H3N2/1-1409, 2012.93634497 69 | A/Alaska/16/2012|KC892528|07/13/2012|USA||H3N2/1-1409, 2012.5338809 70 | A/Auckland/608/2002|CY022551|06/08/2002|New_Zealand||H3N2/5-1413, 2002.43531828 71 | A/Colorado/17/2012|KC892646|06/21/2012|USA||H3N2/1-1409, 2012.47364819 72 | A/Memphis/103/74|CY006829|1974|USA||H3N2/8-1416, 1974.00273785 73 | A/HaNoi/BT251/2007|CY105504|07/26/2007|Viet_Nam||H3N2/5-1413, 2007.56673511 74 | A/Managua/3587.02/2010|CY098075|06/03/2010|Nicaragua||H3N2/4-1412, 2010.42162902 75 | A/HaNoi/Q492/2007|CY105704|07/10/2007|Viet_Nam||H3N2/4-1412, 2007.5229295 76 | A/Canterbury/233/2005|CY008582|07/24/2005|New_Zealand||H3N2/8-1416, 2005.56125941 77 | A/Stockholm/12/1988|CY113399|1988|Sweden||H3N2/4-1412, 1988.00273785 78 | A/Ohio/UR07_0005/2008|CY037481|02/12/2008|USA|07_08|H3N2/1-1409, 2008.11772758 79 | A/Pennsylvania/08/2010|KC535483|07/27/2010|USA||H3N2/1-1409, 2010.56947296 80 | A/Memphis/4/77|CY008125|1977|USA||H3N2/8-1416, 1977.00273785 81 | A/Pennsylvania/13/2008|GQ369891|12/11/2008|USA|08_09|H3N2/1-1409, 2008.94729637 82 | A/Singapore/C2011.496/2011|KF014483|06/30/2011|Singapore||H3N2/20-1428, 2011.49555099 83 | A/Hong_Kong/H090_739_V3|JN256779|07/29/2009|Hong_Kong||H3N2/1-1409, 2009.57494867 84 | A/Memphis/1/1971|AB101675|1971|USA||H3N2/1-1409, 1971.00273785 85 | A/Utah/11/2011|KC883015|03/10/2011|USA|10_11|H3N2/1-1409, 2011.1889117 86 | A/Peru/PER354/2012|CY163050|05/21/2012|Peru||H3N2/8-1416, 2012.38877481 87 | A/Boston/DOA2_115/2012|CY148446|12/05/2012|USA|12_13|H3N2/1-1409, 2012.93086927 88 | A/New_York/716/1994|CY011890|01/17/1994|USA|93_94|H3N2/2-1410, 1994.04654346 89 | A/Singapore/H2011.751/2011|KF014459|10/01/2011|Singapore||H3N2/20-1428, 2011.75017112 90 | A/Canterbury/418/2003|CY007117|07/15/2003|New_Zealand||H3N2/8-1416, 2003.53661875 91 | A/Peru/PER273/2011|CY162426|08/19/2011|Peru||H3N2/8-1416, 2011.63244353 92 | A/Singapore/H2009.332C/2009|KF014421|05/01/2009|Singapore||H3N2/20-1428, 2009.33127995 93 | A/Western_Australia/42/2003|CY015814|09/17/2003|Australia||H3N2/5-1413, 2003.7118412 94 | A/New_York/674/1995|CY011554|01/19/1995|USA|94_95|H3N2/8-1416, 1995.05201916 95 | A/Hong_Kong/CUHK41757/1997|EU857287|12/30/1997|Hong_Kong||H3N2/1-1409, 1997.99657769 96 | A/Dunedin/10/2002|CY011402|07/09/2002|New_Zealand||H3N2/1-1409, 2002.52019165 97 | A/California/VRDL335/2009|CY068611|05/03/2009|USA||H3N2/4-1412, 2009.33675565 98 | A/North_Carolina/01/2008|EU852002|02/11/2008|USA|07_08|H3N2/1-1409, 2008.11498973 99 | A/California/VRDL233/2009|CY068275|04/29/2009|USA|08_09|H3N2/4-1412, 2009.32580424 100 | A/Texas/JMM_39/2012|CY135014|11/30/2012|USA|12_13|H3N2/8-1416, 2012.91718001 101 | A/New_York/3139/2009|CY050630|04/29/2009|USA|08_09|H3N2/1-1409, 2009.32580424 102 | A/Waikato/6/2000|CY013050|09/08/2000|New_Zealand||H3N2/3-1411, 2000.6899384 103 | A/Peru/PER333/2011|CY162890|09/30/2011|Peru||H3N2/8-1416, 2011.74743326 104 | A/Peru/PER077/2010|CY160898|11/16/2010|Peru||H3N2/8-1416, 2010.87611225 105 | A/Singapore/GP1541/2011|CY124232|09/29/2011|Singapore||H3N2/16-1424, 2011.74469541 106 | A/Mexico/24014/2008|CY147669|12/01/2008|Mexico||H3N2/1-1409, 2008.91991786 107 | A/Texas/03/2008|EU716515|01/17/2008|USA|07_08|H3N2/1-1409, 2008.04654346 108 | A/Nebraska/02/2011|KC883200|01/07/2011|USA|10_11|H3N2/1-1409, 2011.01916496 109 | A/Denmark/54/2006|EU103858|2006|Denmark||H3N2/1-1409, 2006.00273785 110 | A/New_York/712/1993|CY011874|12/02/1993|USA|93_94|H3N2/8-1416, 1993.91991786 111 | A/Hawaii/16/2012|KC892663|08/04/2012|USA||H3N2/1-1409, 2012.59411362 112 | A/England/944/2003|CY088192|11/17/2003|United_Kingdom|03_04|H3N2/1-1409, 2003.8788501 113 | A/Novosibirsk/22/2012|KC135507|02/20/2012|Russia|11_12|H3N2/1-1409, 2012.13963039 114 | A/Alaska/21/2012|KC892659|08/01/2012|USA||H3N2/1-1409, 2012.58590007 115 | A/Peru/PER238/2011|CY162170|08/22/2011|Peru||H3N2/8-1416, 2011.64065708 116 | A/Memphis/2/77|CY008117|1977|USA||H3N2/8-1416, 1977.00273785 117 | A/Managua/5806.01/2010|CY070929|06/08/2010|Nicaragua||H3N2/4-1412, 2010.43531828 118 | A/New_Mexico/09/2012|KC892210|03/15/2012|USA|11_12|H3N2/1-1409, 2012.20533881 119 | A/New_York/738/1994|CY012986|02/04/1994|USA|93_94|H3N2/8-1416, 1994.09582478 120 | A/Texas/NHRC0001/2006|CY091039|02/13/2006|USA||H3N2/4-1412, 2006.12046543 121 | A/Denmark/41/03|AY531015|2003|Denmark||H3N2/1-1409, 2003.00273785 122 | A/Kentucky/UR07_0038/2008|CY039425|02/18/2008|USA|07_08|H3N2/1-1409, 2008.13415469 123 | A/Singapore/GP1362/2011|CY124204|07/29/2011|Singapore||H3N2/16-1424, 2011.57494867 124 | A/Missouri/NHRC0001/2002|CY091095|01/09/2002|USA|01_02|H3N2/4-1412, 2002.02464066 125 | A/Canterbury/417/2003|CY007109|07/15/2003|New_Zealand||H3N2/8-1416, 2003.53661875 126 | A/Hong_Kong/CUHK75994/2003|EU857370|12/20/2003|Hong_Kong||H3N2/1-1409, 2003.96919918 127 | A/Mississippi/UR07_0024/2008|CY039417|02/14/2008|USA|07_08|H3N2/1-1409, 2008.12320329 128 | A/Bilthoven/5930/1974|CY113119|1974|Netherlands||H3N2/4-1412, 1974.00273785 129 | A/Hong_Kong/CUHK53005/2006|EU857330|03/04/2006|Hong_Kong||H3N2/1-1409, 2006.1724846 130 | A/California/VRDL317/2009|CY068515|05/06/2009|USA||H3N2/4-1412, 2009.3449692 131 | A/Peru/PER244/2011|CY162210|08/26/2011|Peru||H3N2/8-1416, 2011.65160849 132 | A/Georgia/NHRC0001/2002|CY091111|02/02/2002|USA|01_02|H3N2/4-1412, 2002.09034908 133 | A/California/04/2013|KF790154|01/06/2013|USA|12_13|H3N2/1-1409, 2013.0164271 134 | A/Australia/19/2009|CY061900|07/21/2009|Australia||H3N2/1-1409, 2009.55304586 135 | A/Delaware/04/2010|KC535490|08/17/2010|USA||H3N2/1-1409, 2010.62696783 136 | A/California/VRDL261/2009|CY068339|05/02/2009|USA||H3N2/4-1412, 2009.3340178 137 | A/Oregon/14/2009|KC535305|06/07/2009|USA|08_09|H3N2/1-1409, 2009.43258042 138 | A/Wisconsin/13/2012|KC892595|05/05/2012|USA|11_12|H3N2/1-1409, 2012.3449692 139 | A/Singapore/GP1810/2011|CY124276|12/01/2011|Singapore||H3N2/20-1428, 2011.91718001 140 | A/Hong_Kong/JY2/1968|CY147440|1968|Hong_Kong||H3N2/8-1416, 1968.00273785 141 | A/Utah/15/2012|KC892709|05/16/2012|USA|11_12|H3N2/1-1409, 2012.37508556 142 | A/Netherlands/414/1998|CY112895|05/12/1998|Netherlands|97_98|H3N2/4-1412, 1998.3613963 143 | A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409, 2011.95550992 144 | A/England/531/2003|CY088232|11/20/2003|United_Kingdom|03_04|H3N2/1-1409, 2003.88706366 145 | A/Wyoming/18/2012|KF790094|10/05/2012|USA|12_13|H3N2/1-1409, 2012.76386037 146 | A/Hong_Kong/H090_674_V1|JN256747|07/07/2009|Hong_Kong||H3N2/1-1409, 2009.51471595 147 | A/Delaware/06/2010|KC882831|11/30/2010|USA|10_11|H3N2/1-1409, 2010.91444216 148 | A/Maine/02/2010|KC882540|12/28/2010|USA|10_11|H3N2/1-1409, 2010.99110198 149 | A/New_York/463/2005|CY003642|02/09/2005|USA|04_05|H3N2/18-1426, 2005.10951403 150 | A/Singapore/H2009.518/2009|KF014425|07/08/2009|Singapore||H3N2/20-1428, 2009.5174538 151 | A/Netherlands/165/1993|CY114063|03/05/1993|Netherlands|92_93|H3N2/4-1412, 1993.17522245 152 | A/Hong_Kong/HKU28/2004|CY043746|07/17/2004|Hong_Kong||H3N2/1-1409, 2004.54483231 153 | A/Missouri/NHRC0001/2006|CY091079|04/05/2006|USA|05_06|H3N2/4-1412, 2006.26009582 154 | A/New_York/384/2005|CY002466|01/06/2005|USA|04_05|H3N2/18-1426, 2005.0164271 155 | A/Malaysia/1965896/2008|CY119044|03/19/2008|Malaysia||H3N2/4-1412, 2008.21629021 156 | A/Boston/DOA2_175/2013|CY148878|01/06/2013|USA|12_13|H3N2/1-1409, 2013.0164271 157 | A/Wellington/27/2004|CY013479|09/11/2004|New_Zealand||H3N2/5-1413, 2004.69815195 158 | A/Hong_Kong/H090_763_V23/2009|CY115802|08/03/2009|Hong_Kong||H3N2/8-1416, 2009.58863792 159 | A/New_York/448/1998|CY003562|11/23/1998|USA|98_99|H3N2/20-1428, 1998.89527721 160 | A/California/UR06_0565/2007|CY026789|03/07/2007|USA|06_07|H3N2/5-1413, 2007.18069815 161 | A/Vermont/UR06_0471/2007|CY025605|02/28/2007|USA|06_07|H3N2/5-1413, 2007.1615332 162 | A/Malaysia/25920/2003|CY118676|09/30/2003|Malaysia||H3N2/4-1412, 2003.74743326 163 | A/New_York/785/1993|CY013210|03/26/1993|USA|92_93|H3N2/5-1413, 1993.23271732 164 | A/Brisbane/10/2007|CY035024|02/06/2007|Australia||H3N2/1-1409, 2007.10130048 165 | A/Hong_Kong/CUHK22163/2000|EU857207|03/05/2000|Hong_Kong||H3N2/1-1409, 2000.1779603 166 | A/Boston/DOA2_189/2013|CY148982|01/14/2013|USA|12_13|H3N2/1-1409, 2013.03832991 167 | A/North_Carolina/01/2011|KC882594|02/01/2011|USA|10_11|H3N2/1-1409, 2011.08761123 168 | A/Peru/PER380/2010|CY163242|10/13/2010|Peru||H3N2/8-1416, 2010.78302533 169 | A/Texas/JMM_57/2012|CY135142|12/07/2012|USA|12_13|H3N2/1-1409, 2012.93634497 170 | A/Peru/PER067/2011|CY160818|10/31/2011|Peru||H3N2/8-1416, 2011.83230664 171 | A/Queensland/50/2004|CY020047|10/27/2004|Australia||H3N2/5-1413, 2004.82409309 172 | A/Memphis/1/80|CY008662|1980|USA||H3N2/8-1416, 1980.00273785 173 | A/Bogota/WRAIR3457N/2010|CY093409|12/01/2010|Colombia||H3N2/4-1412, 2010.91718001 174 | A/Canterbury/16/2004|CY007357|08/06/2004|New_Zealand||H3N2/8-1416, 2004.59958932 175 | A/New_York/352/2005|CY002722|01/04/2005|USA|04_05|H3N2/1-1409, 2005.0109514 176 | A/New_York/433/2000|CY003250|01/05/2000|USA|99_00|H3N2/20-1428, 2000.01368925 177 | A/Denmark/116/2003|EU103879|2003|Denmark||H3N2/1-1409, 2003.00273785 178 | A/Ontario/C37332/2011|JQ658965|01/12/2011|Canada|10_11|H3N2/1-1409, 2011.03285421 179 | A/Indiana/09/2011|KC892993|10/03/2011|USA|11_12|H3N2/1-1409, 2011.75564682 180 | A/Hong_Kong/H090_734_V3|JN256773|07/27/2009|Hong_Kong||H3N2/1-1409, 2009.56947296 181 | A/Bilthoven/6545/1976|CY113223|1976|Netherlands||H3N2/4-1412, 1976.00273785 182 | A/Hong_Kong/CUHK16614/1998|EU857152|07/13/1998|Hong_Kong||H3N2/1-1409, 1998.53114305 183 | A/Canterbury/440/2003|CY007237|08/05/2003|New_Zealand||H3N2/8-1416, 2003.59411362 184 | A/Malaysia/33386/2005|CY118868|12/30/2005|Malaysia||H3N2/4-1412, 2005.99657769 185 | A/New_Mexico/02/2012|KC892371|01/24/2012|USA|11_12|H3N2/1-1409, 2012.06570842 186 | A/New_York/3148/2009|CY050654|2009|USA||H3N2/1-1409, 2009.00273785 187 | A/New_York/698/1995|CY011354|01/31/1995|USA|94_95|H3N2/8-1416, 1995.08487337 188 | A/New_York/23/2003|CY000195|12/16/2003|USA|03_04|H3N2/20-1428, 2003.95824778 189 | A/Hong_Kong/CUHK35435/2004|EU857276|06/10/2004|Hong_Kong||H3N2/1-1409, 2004.44353183 190 | A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409, 2011.98562628 191 | A/Hong_Kong/CUHK4542/1997|EU857296|04/02/1997|Hong_Kong||H3N2/1-1409, 1997.25188227 192 | A/New_York/778/1993|CY012770|02/02/1993|USA|92_93|H3N2/5-1413, 1993.09034908 193 | A/Queensland/24/2002|CY017549|07/25/2002|Australia||H3N2/5-1413, 2002.56399726 194 | A/Boston/DOA2_244/2013|CY149310|01/28/2013|USA|12_13|H3N2/1-1409, 2013.07665982 195 | A/Hue/H521/2007|CY105552|12/07/2007|Viet_Nam||H3N2/4-1412, 2007.93360712 196 | A/Peru/PER036/2011|CY160570|08/29/2011|Peru||H3N2/8-1416, 2011.65982204 197 | A/Peru/PER030/2010|CY160522|11/20/2010|Peru||H3N2/8-1416, 2010.88706366 198 | A/New_York/761/1993|CY012154|03/03/1993|USA|92_93|H3N2/8-1416, 1993.16974675 199 | A/Singapore/C2011.573/2011|KF014488|07/28/2011|Singapore||H3N2/20-1428, 2011.57221081 200 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_200.nwk: -------------------------------------------------------------------------------- 1 | (A/California/UR06_0565/2007|CY026789|03/07/2007|USA|06_07|H3N2/5-1413:0.00071,(((A/Pennsylvania/04/2007|EU516043|03/03/2007|USA|06_07|H3N2/1-1409:0.00142,A/Vermont/UR06_0471/2007|CY025605|02/28/2007|USA|06_07|H3N2/5-1413:0.00214)0.829:0.00071,(((A/Australia/19/2009|CY061900|07/21/2009|Australia||H3N2/1-1409:0.00644,(((A/California/VRDL317/2009|CY068515|05/06/2009|USA||H3N2/4-1412:0.00143,((((A/New_York/3139/2009|CY050630|04/29/2009|USA|08_09|H3N2/1-1409:0.00142,A/New_York/3148/2009|CY050654|2009|USA||H3N2/1-1409:0.00071)0.835:0.00071,((A/Hong_Kong/H090_763_V2|JN256790|08/03/2009|Hong_Kong||H3N2/1-1409:0.0,A/Hong_Kong/H090_763_V23/2009|CY115802|08/03/2009|Hong_Kong||H3N2/8-1416:0.0):0.00055,(A/Hong_Kong/H090_739_V3|JN256779|07/29/2009|Hong_Kong||H3N2/1-1409:0.00142,A/Hong_Kong/H090_734_V3|JN256773|07/27/2009|Hong_Kong||H3N2/1-1409:0.00142)0.904:0.00142)0.812:0.00071)0.927:0.00055,((A/Singapore/C2009.515/2009|KF014467|07/07/2009|Singapore||H3N2/20-1428:0.00142,A/Singapore/H2009.518/2009|KF014425|07/08/2009|Singapore||H3N2/20-1428:0.00071)0.892:0.00055,A/Singapore/H2009.332C/2009|KF014421|05/01/2009|Singapore||H3N2/20-1428:0.00055)0.000:0.00055)0.000:0.00055,(A/Oregon/14/2009|KC535305|06/07/2009|USA|08_09|H3N2/1-1409:0.00214,A/Texas/40/2009|GQ895023|02/24/2009|USA|08_09|H3N2/1-1409:0.00071)0.462:0.00055)0.840:0.00071)0.981:0.00357,A/Kentucky/UR07_0148/2008|CY038857|03/10/2008|USA|07_08|H3N2/1-1409:0.00214)0.990:0.00055,((A/Novosibirsk/707/2009|CY053673|03/2009|Russia|08_09|H3N2/16-1424:0.00214,(A/California/VRDL183/2009|CY068696|04/27/2009|USA|08_09|H3N2/4-1412:0.00143,A/California/VRDL261/2009|CY068339|05/02/2009|USA||H3N2/4-1412:0.00214)0.821:0.00071)0.896:0.00142,((A/California/VRDL233/2009|CY068275|04/29/2009|USA|08_09|H3N2/4-1412:0.00142,(A/Pennsylvania/13/2008|GQ369891|12/11/2008|USA|08_09|H3N2/1-1409:0.00055,A/South_Carolina/07/2008|GQ385873|12/31/2008|USA|08_09|H3N2/1-1409:0.00055)0.957:0.00055)0.891:0.00142,((((A/Boston/DOA24/2011|CY116709|02/01/2011|USA|10_11|H3N2/4-1412:0.00214,A/Maine/02/2010|KC882540|12/28/2010|USA|10_11|H3N2/1-1409:0.00214)0.818:0.00071,((A/Kentucky/11/2010|KC883205|10/18/2010|USA|10_11|H3N2/1-1409:0.0,A/Delaware/04/2010|KC535490|08/17/2010|USA||H3N2/1-1409:0.0):0.00055,A/North_Carolina/01/2011|KC882594|02/01/2011|USA|10_11|H3N2/1-1409:0.00071)0.407:0.00055)0.984:0.00357,(((A/North_Carolina/10/2011|KC892419|12/01/2011|USA|11_12|H3N2/1-1409:0.00428,((A/Singapore/C2011.641/2011|KF014491|08/22/2011|Singapore||H3N2/20-1428:0.00142,A/Singapore/H2011.507/2011|KF014518|07/04/2011|Singapore||H3N2/20-1428:0.00071)0.903:0.00055,((A/Singapore/GP1583/2011|CY124238|10/07/2011|Singapore||H3N2/20-1428:0.00071,A/Cambodia/V1013305/2011|KC118547|10/10/2011|Cambodia||H3N2/1-1409:0.00142)0.909:0.00055,A/Singapore/GP1382/2011|CY124208|08/03/2011|Singapore||H3N2/20-1428:0.00055)0.000:0.00055)0.977:0.00055)0.999:0.00572,((A/Moscow/02/2012|JQ988034|02/01/2012|Russia|11_12|H3N2/22-1430:0.00429,(A/Singapore/GP1810/2011|CY124276|12/01/2011|Singapore||H3N2/20-1428:0.00071,(A/Novosibirsk/22/2012|KC135507|02/20/2012|Russia|11_12|H3N2/1-1409:0.00055,(A/Hawaii/16/2012|KC892663|08/04/2012|USA||H3N2/1-1409:0.00071,(((A/Boston/DOA2_110/2012|CY148406|12/07/2012|USA|12_13|H3N2/1-1409:0.00071,(A/Nebraska/02/2013|KF790067|01/02/2013|USA|12_13|H3N2/1-1409:0.00143,A/Boston/DOA2_158/2013|CY148766|01/03/2013|USA|12_13|H3N2/1-1409:0.00071)0.984:0.00357)0.938:0.00055,(A/Alaska/21/2012|KC892659|08/01/2012|USA||H3N2/1-1409:0.00142,(A/California/04/2013|KF790154|01/06/2013|USA|12_13|H3N2/1-1409:0.00214,A/Texas/JMM_57/2012|CY135142|12/07/2012|USA|12_13|H3N2/1-1409:0.00142)0.899:0.00142)0.967:0.00055)0.000:0.00055,(((A/Colorado/17/2012|KC892646|06/21/2012|USA||H3N2/1-1409:0.00055,A/Wyoming/18/2012|KF790094|10/05/2012|USA|12_13|H3N2/1-1409:0.00214)0.435:0.00055,A/Boston/DOA2_115/2012|CY148446|12/05/2012|USA|12_13|H3N2/1-1409:0.00071)0.000:0.00055,((A/Iowa/14/2012|KF790285|10/18/2012|USA|12_13|H3N2/1-1409:0.00071,(A/Boston/DOA2_104/2012|CY148358|12/22/2012|USA|12_13|H3N2/1-1409:0.00285,(A/Boston/DOA2_244/2013|CY149310|01/28/2013|USA|12_13|H3N2/1-1409:0.00142,(A/Mississippi/01/2013|KF790359|01/08/2013|USA|12_13|H3N2/1-1409:0.00055,A/California/14/2013|KF789566|01/29/2013|USA|12_13|H3N2/1-1409:0.00055)0.889:0.00055)0.807:0.00071)0.818:0.00071)0.940:0.00055,(A/Boston/DOA2_175/2013|CY148878|01/06/2013|USA|12_13|H3N2/1-1409:0.00428,A/Boston/DOA2_189/2013|CY148982|01/14/2013|USA|12_13|H3N2/1-1409:0.00142)1.000:0.00055)0.000:0.00055)0.000:0.00055)0.953:0.00055)0.786:0.00071)0.928:0.00055)0.772:0.00071)0.941:0.00214,(A/Saint_Petersburg/RII03/2012|CY114550|02/06/2012|Russia|11_12|H3N2/9-1417:0.00214,((A/Alaska/16/2012|KC892528|07/13/2012|USA||H3N2/1-1409:0.00055,(A/Peru/PER354/2012|CY163050|05/21/2012|Peru||H3N2/8-1416:0.00142,(A/Wisconsin/13/2012|KC892595|05/05/2012|USA|11_12|H3N2/1-1409:0.00071,A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409:0.00055)0.922:0.00142)0.970:0.00055)0.000:0.00055,(((A/Singapore/C2011.496/2011|KF014483|06/30/2011|Singapore||H3N2/20-1428:0.00055,(A/Singapore/GP1362/2011|CY124204|07/29/2011|Singapore||H3N2/16-1424:0.00055,A/Singapore/C2011.573/2011|KF014488|07/28/2011|Singapore||H3N2/20-1428:0.00055)0.780:0.00071)0.816:0.00071,A/Singapore/GP1797/2011|CY124274|11/29/2011|Singapore||H3N2/20-1428:0.00071)0.944:0.00055,(A/Singapore/GP1541/2011|CY124232|09/29/2011|Singapore||H3N2/16-1424:0.00214,A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409:0.00214)0.990:0.00055)0.000:0.00055)0.984:0.00055)0.945:0.00214)0.138:0.00055)0.942:0.00214,(A/Managua/3587.02/2010|CY098075|06/03/2010|Nicaragua||H3N2/4-1412:0.00055,A/Managua/5806.01/2010|CY070929|06/08/2010|Nicaragua||H3N2/4-1412:0.00071)0.982:0.00285)0.000:0.00055)0.972:0.00285,((A/California/VRDL335/2009|CY068611|05/03/2009|USA||H3N2/4-1412:0.00569,(A/Peru/PER251/2010|CY162258|10/12/2010|Peru||H3N2/8-1416:0.00055,A/Peru/PER030/2010|CY160522|11/20/2010|Peru||H3N2/8-1416:0.00140)0.966:0.00357)0.846:0.00055,((A/Nebraska/02/2011|KC883200|01/07/2011|USA|10_11|H3N2/1-1409:0.00050,(A/Texas/JMM_39/2012|CY135014|11/30/2012|USA|12_13|H3N2/8-1416:0.00552,A/New_Mexico/02/2012|KC892371|01/24/2012|USA|11_12|H3N2/1-1409:0.00234)0.832:0.00214)0.930:0.00055,(((((A/Delaware/06/2010|KC882831|11/30/2010|USA|10_11|H3N2/1-1409:0.00214,A/Pennsylvania/08/2010|KC535483|07/27/2010|USA||H3N2/1-1409:0.00142)0.679:0.00055,A/Peru/PER380/2010|CY163242|10/13/2010|Peru||H3N2/8-1416:0.00055)0.000:0.00055,((A/Utah/11/2011|KC883015|03/10/2011|USA|10_11|H3N2/1-1409:0.00354,((A/Peru/PER388/2011|CY163306|09/14/2011|Peru||H3N2/8-1416:0.00142,(A/Peru/PER333/2011|CY162890|09/30/2011|Peru||H3N2/8-1416:0.00055,A/Peru/PER244/2011|CY162210|08/26/2011|Peru||H3N2/8-1416:0.00071)0.170:0.00055)0.946:0.00214,((A/Peru/PER395/2011|CY163362|10/24/2011|Peru||H3N2/8-1416:0.00142,(((A/Peru/PER238/2011|CY162170|08/22/2011|Peru||H3N2/8-1416:0.0,A/Peru/PER036/2011|CY160570|08/29/2011|Peru||H3N2/8-1416:0.0):0.00055,A/Peru/PER067/2011|CY160818|10/31/2011|Peru||H3N2/8-1416:0.00071)0.799:0.00071,(A/Peru/PER273/2011|CY162426|08/19/2011|Peru||H3N2/8-1416:0.00071,(A/Peru/PER389/2012|CY163314|04/02/2012|Peru||H3N2/8-1416:0.00055,A/Peru/PER077/2010|CY160898|11/16/2010|Peru||H3N2/8-1416:0.00071)0.969:0.00285)0.869:0.00055)0.375:0.00055)0.945:0.00214,A/Boston/DOA01/2011|CY111128|01/03/2011|USA|10_11|H3N2/4-1412:0.00357)0.241:0.00055)0.842:0.00055)0.381:0.00071,A/Bogota/WRAIR3457N/2010|CY093409|12/01/2010|Colombia||H3N2/4-1412:0.00211)0.901:0.00055)0.000:0.00055,(A/Singapore/H2011.751/2011|KF014459|10/01/2011|Singapore||H3N2/20-1428:0.00285,A/Ontario/C37332/2011|JQ658965|01/12/2011|Canada|10_11|H3N2/1-1409:0.00055)0.807:0.00071)0.000:0.00055,(A/Guangdong/460/2010|CY091846|10/22/2010|China||H3N2/20-1428:0.00142,(A/Indiana/09/2011|KC892993|10/03/2011|USA|11_12|H3N2/1-1409:0.00071,(A/Colorado/07/2011|KC892191|10/23/2011|USA|11_12|H3N2/1-1409:0.00055,(A/Utah/15/2012|KC892709|05/16/2012|USA|11_12|H3N2/1-1409:0.00214,A/New_Mexico/09/2012|KC892210|03/15/2012|USA|11_12|H3N2/1-1409:0.00143)0.340:0.00055)0.826:0.00071)0.974:0.00285)0.953:0.00055)0.750:0.00055)0.773:0.00071)0.194:0.00055)0.886:0.00142)0.935:0.00214)0.950:0.00055)0.736:0.00055)0.728:0.00055,(A/Texas/03/2008|EU716515|01/17/2008|USA|07_08|H3N2/1-1409:0.00251,(A/Hong_Kong/H090_674_V1|JN256747|07/07/2009|Hong_Kong||H3N2/1-1409:0.00679,A/Malaysia/1965896/2008|CY119044|03/19/2008|Malaysia||H3N2/4-1412:0.00324)0.675:0.00142)0.711:0.00055)0.406:0.00071,(A/North_Carolina/01/2008|EU852002|02/11/2008|USA|07_08|H3N2/1-1409:0.00071,((A/Kentucky/UR07_0038/2008|CY039425|02/18/2008|USA|07_08|H3N2/1-1409:0.00071,A/Hue/H521/2007|CY105552|12/07/2007|Viet_Nam||H3N2/4-1412:0.00142)0.919:0.00055,((A/Mississippi/UR07_0024/2008|CY039417|02/14/2008|USA|07_08|H3N2/1-1409:0.00071,A/Ohio/UR07_0005/2008|CY037481|02/12/2008|USA|07_08|H3N2/1-1409:0.00142)0.276:0.00055,A/HaNoi/BT251/2007|CY105504|07/26/2007|Viet_Nam||H3N2/5-1413:0.00071)0.000:0.00055)0.728:0.00055)1.000:0.00055)0.909:0.00055)0.867:0.00055,(A/Kentucky/UR06_0158/2007|CY026885|02/05/2007|USA|06_07|H3N2/5-1413:0.00055,((A/Texas/UR06_0358/2007|CY027565|02/20/2007|USA|06_07|H3N2/5-1413:0.00071,(A/New_York/UR07_0080/2008|CY036969|02/25/2008|USA|07_08|H3N2/1-1409:0.00142,A/Mexico/24014/2008|CY147669|12/01/2008|Mexico||H3N2/1-1409:0.00285)0.829:0.00071)0.830:0.00071,(A/Brisbane/10/2007|CY035024|02/06/2007|Australia||H3N2/1-1409:0.00142,(A/Malaysia/1681079/2006|CY118940|11/24/2006|Malaysia||H3N2/4-1412:0.00214,((A/New_York/352/2005|CY002722|01/04/2005|USA|04_05|H3N2/1-1409:0.00430,(A/Texas/NHRC0001/2006|CY091039|02/13/2006|USA||H3N2/4-1412:0.00071,A/Missouri/NHRC0001/2006|CY091079|04/05/2006|USA|05_06|H3N2/4-1412:0.00286)0.985:0.00430)0.892:0.00141,((A/New_York/381/2004|CY002250|12/28/2004|USA|04_05|H3N2/18-1426:0.00430,A/New_York/463/2005|CY003642|02/09/2005|USA|04_05|H3N2/18-1426:0.00142)0.783:0.00071,(((((((A/Hong_Kong/CUHK22163/2000|EU857207|03/05/2000|Hong_Kong||H3N2/1-1409:0.00214,(A/New_York/433/2000|CY003250|01/05/2000|USA|99_00|H3N2/20-1428:0.00071,A/Waikato/6/2000|CY013050|09/08/2000|New_Zealand||H3N2/3-1411:0.00142)0.048:0.00055)0.941:0.00223,(((((A/Georgia/NHRC0001/2002|CY091111|02/02/2002|USA|01_02|H3N2/4-1412:0.00214,((A/Malaysia/25920/2003|CY118676|09/30/2003|Malaysia||H3N2/4-1412:0.00071,((A/Canterbury/417/2003|CY007109|07/15/2003|New_Zealand||H3N2/8-1416:0.00071,((A/Australia/NHRC0008/2003|CY091279|07/08/2003|Australia||H3N2/4-1412:0.0,A/Canterbury/418/2003|CY007117|07/15/2003|New_Zealand||H3N2/8-1416:0.0):0.00055,(A/Canterbury/404/2003|CY007045|07/05/2003|New_Zealand||H3N2/8-1416:0.00071,A/Canterbury/440/2003|CY007237|08/05/2003|New_Zealand||H3N2/8-1416:0.00071)0.952:0.00055)0.949:0.00055)0.837:0.00071,(A/Hong_Kong/CUHK75994/2003|EU857370|12/20/2003|Hong_Kong||H3N2/1-1409:0.00142,(((A/England/492/2003|CY088288|11/21/2003|United_Kingdom|03_04|H3N2/1-1409:0.00071,A/England/944/2003|CY088192|11/17/2003|United_Kingdom|03_04|H3N2/1-1409:0.00055)0.000:0.00055,(A/Denmark/72/2003|EU103942|2003|Denmark||H3N2/1-1409:0.00142,A/Denmark/120/2003|EU103940|2003|Denmark||H3N2/1-1409:0.00071)0.648:0.00055)0.678:0.00055,A/England/531/2003|CY088232|11/20/2003|United_Kingdom|03_04|H3N2/1-1409:0.00071)0.949:0.00214)0.826:0.00071)0.458:0.00055)0.521:0.00055,(A/Western_Australia/42/2003|CY015814|09/17/2003|Australia||H3N2/5-1413:0.00143,A/New_York/23/2003|CY000195|12/16/2003|USA|03_04|H3N2/20-1428:0.00142)0.902:0.00142)0.970:0.00285)0.272:0.00055,A/Missouri/NHRC0001/2002|CY091095|01/09/2002|USA|01_02|H3N2/4-1412:0.00142)0.956:0.00053,(((A/Waikato/51/2002|CY012058|08/12/2002|New_Zealand||H3N2/8-1416:0.00071,(A/Dunedin/10/2002|CY011402|07/09/2002|New_Zealand||H3N2/1-1409:0.00071,A/Queensland/24/2002|CY017549|07/25/2002|Australia||H3N2/5-1413:0.00071)0.724:0.00055)0.797:0.00071,(A/England/460/2003|CY088088|11/11/2003|United_Kingdom|03_04|H3N2/1-1409:0.00644,A/Auckland/608/2002|CY022551|06/08/2002|New_Zealand||H3N2/5-1413:0.00071)0.899:0.00143)0.930:0.00055,A/New_York/407/2002|CY003426|01/08/2002|USA|01_02|H3N2/8-1416:0.00500)0.441:0.00070)1.000:0.01401,((((A/Hong_Kong/CUHK12794/1997|EU857131|06/11/1997|Hong_Kong||H3N2/1-1409:0.00071,A/Hong_Kong/CUHK4542/1997|EU857296|04/02/1997|Hong_Kong||H3N2/1-1409:0.00071)0.919:0.00230,(A/New_South_Wales/21/1999|CY016557|1999|Australia||H3N2/5-1413:0.00270,A/Hong_Kong/CUHK16614/1998|EU857152|07/13/1998|Hong_Kong||H3N2/1-1409:0.00055)0.998:0.00718)0.859:0.00174,(A/New_York/517/1998|CY006285|01/03/1998|USA|97_98|H3N2/4-1412:0.00814,((A/New_York/320/1999|CY001858|03/26/1999|USA|98_99|H3N2/17-1425:0.00356,A/Netherlands/414/1998|CY112895|05/12/1998|Netherlands|97_98|H3N2/4-1412:0.00055)0.851:0.00055,(A/New_York/448/1998|CY003562|11/23/1998|USA|98_99|H3N2/20-1428:0.00292,A/Hong_Kong/CUHK41757/1997|EU857287|12/30/1997|Hong_Kong||H3N2/1-1409:0.00279)0.211:0.00071)0.987:0.00542)0.505:0.00142)0.868:0.00053,(A/New_York/674/1995|CY011554|01/19/1995|USA|94_95|H3N2/8-1416:0.00357,((((((A/Stockholm/12/1988|CY113399|1988|Sweden||H3N2/4-1412:0.01015,((A/Memphis/3/80|CY008470|1980|USA||H3N2/8-1416:0.0,A/Memphis/1/80|CY008662|1980|USA||H3N2/8-1416:0.0):0.00145,((A/Memphis/4/77|CY008125|1977|USA||H3N2/8-1416:0.0,A/Memphis/2/77|CY008117|1977|USA||H3N2/8-1416:0.0):0.00240,(A/Bilthoven/628/1976|CY113191|1976|Netherlands||H3N2/4-1412:0.00502,((A/Memphis/1/1971|AB101675|1971|USA||H3N2/1-1409:0.00422,A/Hong_Kong/JY2/1968|CY147440|1968|Hong_Kong||H3N2/8-1416:0.02859)0.999:0.00871,((A/Port_chalmers/1/1973|CY009350|1973|New_Zealand||H3N2/8-1416:0.00142,A/Bilthoven/5930/1974|CY113119|1974|Netherlands||H3N2/4-1412:0.00285)0.886:0.00143,(A/Memphis/103/74|CY006829|1974|USA||H3N2/8-1416:0.00718,A/Bilthoven/6545/1976|CY113223|1976|Netherlands||H3N2/4-1412:0.01080)0.794:0.00069)0.888:0.00142)0.917:0.00213)0.994:0.00778)0.997:0.00923)1.000:0.02124)1.000:0.01444,(A/Netherlands/357/1993|CY114071|12/06/1993|Netherlands|93_94|H3N2/4-1412:0.00214,(A/New_York/712/1993|CY011874|12/02/1993|USA|93_94|H3N2/8-1416:0.00055,A/New_York/738/1994|CY012986|02/04/1994|USA|93_94|H3N2/8-1416:0.00142)0.950:0.00214)0.881:0.00143)0.879:0.00143,A/Netherlands/165/1993|CY114063|03/05/1993|Netherlands|92_93|H3N2/4-1412:0.00357)0.823:0.00071,A/New_York/761/1993|CY012154|03/03/1993|USA|92_93|H3N2/8-1416:0.00142)0.188:0.00055,(((A/New_York/716/1994|CY011890|01/17/1994|USA|93_94|H3N2/2-1410:0.00428,(A/New_York/785/1993|CY013210|03/26/1993|USA|92_93|H3N2/5-1413:0.00055,A/New_York/778/1993|CY012770|02/02/1993|USA|92_93|H3N2/5-1413:0.00071)0.659:0.00055)0.787:0.00071,A/Lyon/672/1993|CY113983|02/22/1993|France|92_93|H3N2/4-1412:0.00285)0.000:0.00055,A/Nanchang/0074/94|CY003754|1994|China||H3N2/8-1416:0.00142)0.812:0.00071)0.822:0.00071,(A/New_York/665/1994|CY011522|12/16/1994|USA|94_95|H3N2/8-1416:0.00055,A/New_York/698/1995|CY011354|01/31/1995|USA|94_95|H3N2/8-1416:0.00071)0.978:0.00357)0.955:0.00286)0.999:0.00863)0.997:0.00769)0.941:0.00430,(A/Hong_Kong/CUHK51424/2001|EU857312|12/26/2001|Hong_Kong||H3N2/1-1409:0.00573,((A/Western_Australia/8/2000|CY015662|10/17/2000|Australia||H3N2/1-1409:0.0,A/South_Australia/72/2000|CY021775|2000|Australia||H3N2/1-1409:0.0):0.00055,A/Waikato/1/2001|CY011970|04/25/2001|New_Zealand||H3N2/2-1410:0.00428)0.971:0.00286)0.776:0.00106)0.554:0.00051)1.000:0.01072,(A/Denmark/41/03|AY531015|2003|Denmark||H3N2/1-1409:0.00285,(A/Fujian/445/2003|CY121450|2003|China||H3N2/1-1409:0.00286,(A/Hong_Kong/CUHK71313/2003|EU857364|09/21/2003|Hong_Kong||H3N2/1-1409:0.00142,A/Hong_Kong/HKU28/2004|CY043746|07/17/2004|Hong_Kong||H3N2/1-1409:0.00357)0.976:0.00357)0.782:0.00071)0.789:0.00069)0.998:0.00575,A/Hong_Kong/CUHK35435/2004|EU857276|06/10/2004|Hong_Kong||H3N2/1-1409:0.00429)0.844:0.00070,A/Denmark/116/2003|EU103879|2003|Denmark||H3N2/1-1409:0.00071)0.839:0.00071,((A/Wellington/55/2004|CY020343|09/27/2004|New_Zealand||H3N2/5-1413:0.00071,((A/New_York/384/2005|CY002466|01/06/2005|USA|04_05|H3N2/18-1426:0.0,A/Canterbury/16/2004|CY007357|08/06/2004|New_Zealand||H3N2/8-1416:0.0):0.00055,A/Queensland/50/2004|CY020047|10/27/2004|Australia||H3N2/5-1413:0.00071)0.096:0.00055)0.978:0.00357,A/Wellington/27/2004|CY013479|09/11/2004|New_Zealand||H3N2/5-1413:0.00142)0.327:0.00055)0.873:0.00055,(((A/Malaysia/33386/2005|CY118868|12/30/2005|Malaysia||H3N2/4-1412:0.00214,A/Canterbury/233/2005|CY008582|07/24/2005|New_Zealand||H3N2/8-1416:0.00214)0.984:0.00055,(A/Hong_Kong/CUHK40210/2005|EU857280|06/06/2005|Hong_Kong||H3N2/1-1409:0.00142,A/TayNguyen/TN348/2005|CY105376|08/01/2005|Viet_Nam||H3N2/5-1413:0.00142)0.963:0.00055)0.743:0.00055,(A/Denmark/54/2006|EU103858|2006|Denmark||H3N2/1-1409:0.00502,A/Hong_Kong/CUHK53005/2006|EU857330|03/04/2006|Hong_Kong||H3N2/1-1409:0.00502)0.823:0.00069)0.915:0.00142)0.709:0.00055)0.788:0.00071)0.989:0.00502)0.876:0.00142)0.364:0.00055)0.980:0.00055)0.000:0.00055)0.000:0.00055,(A/HaNoi/Q492/2007|CY105704|07/10/2007|Viet_Nam||H3N2/4-1412:0.00142,A/HaNoi/Q638/2007|CY105736|08/29/2007|Viet_Nam||H3N2/4-1412:0.00142)0.706:0.00055); 2 | -------------------------------------------------------------------------------- /data/h3n2_na/h3n2_na_20_aa.fasta: -------------------------------------------------------------------------------- 1 | >A/Hawaii/02/2013|KF789866|05/28/2013|USA|12_13|H3N2/1-1409 2 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFDSPPNNQVMLCEPTIIER 3 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREP 4 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRBRTPYRTLLMNELGVPFHLGTKQVCIAWSS 5 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 6 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 7 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 8 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 9 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 10 | >A/Boston/DOA2_107/2012|CY148382|11/01/2012|USA|12_13|H3N2/1-1409 11 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 12 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREP 13 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 14 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 15 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 16 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 17 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 18 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 19 | >A/Oregon/15/2009|GQ895004|06/25/2009|USA|08_09|H3N2/1-1409 20 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 21 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 22 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRXRTPYRTLLMNELGVPFHLGTKQVCIAWSS 23 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 24 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 25 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 26 | WMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 27 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 28 | >A/Hong_Kong/H090_695_V10/2009|CY115546|07/10/2009|Hong_Kong||H3N2/8-1416 29 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 30 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 31 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 32 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 33 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 34 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 35 | WMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 36 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMSV 37 | >A/New_York/182/2000|CY001279|02/18/2000|USA|99_00|H3N2/1-1409 38 | MNPNQKIITIGSVSLTIATICFLMQIAILVTTVTLHFKQYECNSPPNNQVMLCEPTIIER 39 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREP 40 | YVSCDPDKCYQFALGQGTTLNNGHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 41 | SSCHDGKAWLHVCVTGDDENATASFIYNGRLVDSIGSWSKKILRTQESECVCINGTCTVV 42 | MTDGSASGKADTKILFIEEGKIVHTSSLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 43 | PIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 44 | WMGRTISEKLRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 45 | CFYVELIRGRKQETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 46 | >A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416 47 | MNPNQKIITIGSVSLTIATICFLMQVAILVTTVTLHFKQYECNSPPNNQVMLCEPTIIER 48 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREP 49 | YVSCDPDKCYQFALGQGTTLNNGHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 50 | SSCHDGKAWLHVCVTGDDENATASFIYNGRLVDSIGSWSKKILRTQESECVCINGTCTVV 51 | MTDGSASGKADTKILFIEEGKIVHTSLLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 52 | PIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 53 | WMGRTISEKLRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 54 | CFYVELIRGRKQETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 55 | >A/Minab/797/2011|KC865620|12/24/2011|Iran||H3N2/20-1428 56 | MNPNQKIITIGSVSLTISTICFFMQIAILMTTVTLHFKQCEFNSPPNNQVMLCEPTIIER 57 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 58 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCMAWSS 59 | SSCHDGKAWLHVCITGNDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 60 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 61 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 62 | WMGRTITETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 63 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 64 | >A/Nebraska/15/2011|KC892583|12/15/2011|USA|11_12|H3N2/1-1409 65 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 66 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 67 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 68 | SSCHDGKAWLHVCITGDDKNATASFIYNGKLVDSVVSWSKEILRTQESECVCINGTCTVV 69 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 70 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 71 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 72 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 73 | >A/New_Hampshire/12/2012|KF790252|11/08/2012|USA|12_13|H3N2/1-1409 74 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 75 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREP 76 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 77 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 78 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 79 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 80 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 81 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 82 | >A/Scotland/76/2003|CY088128|11/03/2003|United_Kingdom|03_04|H3N2/1-1409 83 | MNPNQKIITIGSVSLTIAAICFLMQIAILVTTVTLHFKQHECNSPPNNQVMLCEPTIIER 84 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREP 85 | YVSCDPDKCYQFALGQGTTLNNGHSNDTVHDRTPYRTLLMNELGVPFHLGTRQVCIAWSS 86 | SSCHDGKAWLHVCVTGDDKNATASFIYNGRLVDSIGSWSKKILRTQESECVCINGTCTVV 87 | MTDGSASGKADTKILFIEEGKIVHISTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 88 | PIVDINVKDYSIVSSYVCSGLVGDTPRKNDSFSSSHCLDPNNEEGGHGVKGWAFDDGNDV 89 | WMGRTISEKLRSGYETFKVIEGWSKPNSKLQINRQVIVERGNRSGYSGIFSVEGKSCINR 90 | CFYVELIRGRKEETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 91 | >A/Managua/25/2007|CY032439|06/27/2007|Nicaragua||H3N2/1-1409 92 | MNPNQKIITIGSVSLTISTICFFMQIAILATTVTLHFKQYEFNSPPNNQVMLCEPTIIER 93 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 94 | YVSCDPDKCYQFALGQGTTLNNVHSNDTVRGRTPYRTLLMNELGVPFHLGTKQVCIAWSS 95 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSIVSWSKEILRTQESECVCINGTCTVV 96 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 97 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 98 | WMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDKGNRSGYSGIFSVEGKSCINR 99 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 100 | >A/Boston/57/2008|CY044710|02/24/2008|USA|07_08|H3N2/1-1409 101 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSSPNNQVMLCEPTIIER 102 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 103 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 104 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSIVSWSKEILRTQESECVCINGTCTVV 105 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 106 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 107 | WMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 108 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 109 | >A/DaNang/DN434/2008|CY104616|11/11/2008|Viet_Nam||H3N2/4-1412 110 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 111 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 112 | YVSCDPDKCYQFALGQGTTLNNVHSNDTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 113 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSIVSWSKEILRTQESECVCINGTCTVV 114 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAKHVEECSCYPRHPGVRCVCRDNWKGSNR 115 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 116 | WMGRTISEKSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 117 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 118 | >A/Mexico/InDRE940/2003|CY100628|2003|Mexico||H3N2/15-1423 119 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 120 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREP 121 | YVSCDPDKCYQFALGXGTTLNNVHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 122 | SSCHDGKAWLHVCVTGDDENATASFIYNGRLVDSIVSWSKKILRTQESECVCINGTCTVV 123 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 124 | PIVDINIKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 125 | WMGRTISEKLRSGYETFKVIEGWSNPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 126 | CFYVELIRGRKQETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 127 | >A/Indiana/03/2012|KC892731|04/03/2012|USA|11_12|H3N2/1-1409 128 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 129 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCGITGFAPYSKDNSIRLSAGGDIWVTREP 130 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 131 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 132 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 133 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 134 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 135 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 136 | >A/Maryland/21/2011|KC892695|12/26/2011|USA|11_12|H3N2/1-1409 137 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 138 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 139 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRBRTPYRTLLMNELGVPFHLGTKQVCIAWSS 140 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 141 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 142 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 143 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKSCINR 144 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGANLNLMPI 145 | >A/Denmark/107/2003|EU103941|2003|Denmark||H3N2/1-1409 146 | MNPNQKIITIGSVSLTIATICFLMQIAILVTTVTLHFKQHECNSPPNNQVMLCEPTIIER 147 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREP 148 | YVSCDPDKCYQFALGQGTTLNNGHSNDTVHDRTPYRTLLMNELGVPFHLGTRQVCIAWSS 149 | SSCHDGKAWLHVCVTGDDKNATASFIYNGRLVDSIGSWSKKILRTQESECVCINGTCTVV 150 | MTDGSASGKADTKILFIEEGKIVHISTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 151 | PIVDINVKDYSIVSSYVCSGLVGDTPRKNDSFSSSHCLDPNNEEGGHGVKGWAFDDGNDV 152 | WMGRTISEKLRSGYETFKVIEGWSKPNSKLQINRQVIVERGNRSGYSGIFSVEGKSCINR 153 | CFYVELIRGRKEETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI 154 | >A/Peru/PER247/2011|CY162234|08/26/2011|Peru||H3N2/8-1416 155 | MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 156 | NITEIVYLTNTTIEKEICPKLAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREP 157 | YVSCDPNKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 158 | SSCHDGKAWLHVCITGDDKNATASFIYNGKLVDSVVSWSKEILRTQESECVCINGTCTVV 159 | MTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 160 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 161 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINR 162 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 163 | >A/Maryland/03/2013|KF789621|02/10/2013|USA|12_13|H3N2/1-1409 164 | MNPNQKIITIGSVSLTISTVCFFMQIAILITTVTLHFKQYEFNSPPNNQVMLCEPTIIER 165 | NITEIVYLTNTTIEKEICPKPAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREP 166 | YVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSS 167 | SSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVV 168 | MTDGSASGEADTKILFIEEGKIIHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNR 169 | PIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDV 170 | WMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGDRSGYSGIFSVEGKNCINR 171 | CFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 172 | -------------------------------------------------------------------------------- /data/tb/lee_2015.informative_sites.fasta: -------------------------------------------------------------------------------- 1 | >G22644 2 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 3 | TCGTTCCACCGCACCCACCACCGCTACCCTCGTCAGGGAGCCCCCTGATCGATCCGGCGT 4 | GCCGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 5 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 6 | >G22725 7 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACTTGAGAGACCAAGCGGTAT 8 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 9 | GCAAAGTGGGGCATACGCGCCAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 10 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGCGCTG 11 | >G22684 12 | TTTGCTGCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 13 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCAGTCAGGTAC 14 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 15 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 16 | >G22723 17 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTAAGCGAACCGATCATGC 18 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 19 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 20 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCCG 21 | >G22677 22 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 23 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 24 | GCAAAGTGGGCCATACGCGGGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 25 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 26 | >G22583 27 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 28 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 29 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 30 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 31 | >G22733 32 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 33 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 34 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 35 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 36 | >G22699 37 | CTCGTTCGGCGCGCCACGCTCGAAGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 38 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 39 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 40 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 41 | >G22612 42 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 43 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 44 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 45 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCTG 46 | >G22637 47 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 48 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 49 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 50 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 51 | >G22635 52 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAATCGATCATAC 53 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 54 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 55 | GCGGCCCCCGCTCTCCGGGAACGGTGCCTCGGTCTG 56 | >G22592 57 | CTCGCTCCGAACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGACCGAACCGATCATGC 58 | TCGTTCCACCGCACCAACCANCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 59 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGGGGCAGGGCCAT 60 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 61 | >G22657 62 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 63 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 64 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 65 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 66 | >G22704 67 | TTTGCTGCGCGCGCCACGCCCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 68 | TCGCCCTGCCGCACCACCTACCGCCACCCTCGCCTGGGAACCCTCCGCCCAGTCAGGTAC 69 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCTAT 70 | GCGGCCCTCGCTTTTCTAGGACGGTACCCGGGGCTG 71 | >G22668 72 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 73 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 74 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 75 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 76 | >G22670 77 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 78 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 79 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 80 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 81 | >G22577 82 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 83 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 84 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 85 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 86 | >G22642 87 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 88 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 89 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 90 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 91 | >G22605 92 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 93 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 94 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 95 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 96 | >G22710 97 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 98 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 99 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 100 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 101 | >G22683 102 | TTTGCTGCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 103 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCAGTCAGGTAC 104 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 105 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 106 | >G22597 107 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 108 | TCGTTCCACCGCACCCACCACCGCTACCCTCGTCAGGGAGCCCCCTGATCGATCCGGCGT 109 | GCCGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 110 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 111 | >G22709 112 | CTCGCTCCGAACGCGATACTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 113 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCTAGGGAGCCCCCCGATCGGTTCGGCGC 114 | GCAGAGCGTGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGGGGCAGGGCCAT 115 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 116 | >G22590 117 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 118 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 119 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 120 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 121 | >G22603 122 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 123 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 124 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 125 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 126 | >G22681 127 | TTTGCTGCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 128 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCAGTCAGGTAC 129 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 130 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 131 | >G22584 132 | CTCGCTCCGAACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGACCGAACCGATCATGC 133 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 134 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGGGGCAGGGCCAT 135 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 136 | >G22690 137 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 138 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCTCCCGATCGGTCCGGCGC 139 | GCAGAGCGGGCTATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGTAGGGCCAT 140 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 141 | >G22598 142 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 143 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 144 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 145 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 146 | >G22579 147 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 148 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 149 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 150 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 151 | >G22602 152 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 153 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 154 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 155 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 156 | >G22580 157 | CTCGTTCGGCGCTCCACGNTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 158 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 159 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 160 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 161 | >G22711 162 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 163 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 164 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 165 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 166 | >G22627 167 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 168 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 169 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 170 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 171 | >G22574 172 | CTCGCTCCGCGTGCCACGCTCGCGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 173 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 174 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 175 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 176 | >G22700 177 | CTCGTTCGGCGCGCCACGCTCGAAGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 178 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 179 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 180 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 181 | >G22730 182 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 183 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 184 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 185 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCTG 186 | >G22595 187 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 188 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 189 | GCAGAGCGGGCCNTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 190 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCNG 191 | >G22663 192 | CTCGCTCCGAACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 193 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 194 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 195 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 196 | >G22658 197 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 198 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 199 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 200 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 201 | >G22568 202 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 203 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 204 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 205 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 206 | >G22689 207 | CTCGTTCCACGCGCCACGCTCGAGGTCCCGTCTGAAGGGACCTGAGAGACCAAGCGGTAT 208 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAAGGAACCCCCCGCCCGGTCAGGTAC 209 | GCAAAGTGGGCCAGACGCGGGGATACTGTCGACACGGGATTCAATGGGTGACGGGGCCAT 210 | GCGGACCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 211 | >G22674 212 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 213 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 214 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 215 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 216 | >G22667 217 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 218 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 219 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 220 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 221 | >G22673 222 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 223 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 224 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 225 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 226 | >G22609 227 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 228 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 229 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 230 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 231 | >G22625 232 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 233 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATATAC 234 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 235 | GCGGCTCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 236 | >G22664 237 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 238 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 239 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 240 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 241 | >G22666 242 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 243 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 244 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 245 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 246 | >G22726 247 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACTTGAGAGACCAAGCGGTAT 248 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 249 | GCAAAGTGGGGCATACGCGCCAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 250 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGCGCTG 251 | >G22623 252 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 253 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 254 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 255 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 256 | >G22680 257 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 258 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 259 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 260 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 261 | >G22618 262 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 263 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 264 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 265 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 266 | >G22682 267 | TTTGCTGCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 268 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCAGTCAGGTAC 269 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 270 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 271 | >G22685 272 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 273 | TCGCCCCGACGCACCAACCGNCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 274 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 275 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 276 | >G22614 277 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 278 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 279 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 280 | GCGGCTCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 281 | >G22643 282 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 283 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 284 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 285 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCTG 286 | >G22732 287 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 288 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 289 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 290 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 291 | >G22576 292 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 293 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 294 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 295 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCCG 296 | >G22724 297 | CTCGTTCGGCGCGCCACGCTCGAAGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 298 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 299 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 300 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 301 | >G22708 302 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAATCGATCATAC 303 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 304 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 305 | GCGGCCCCCGCTCTCCGGGAACGGTGCCTCGGTCTG 306 | >G22693 307 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 308 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCTCCCGATCGGTCCGGCGC 309 | GCAGAGCGGGCTATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGTAGGGCCAT 310 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 311 | >G22615 312 | CTCGCTCCGCGCGCCCCGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 313 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 314 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 315 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 316 | >G22607 317 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 318 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 319 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 320 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 321 | >G22638 322 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 323 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 324 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 325 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 326 | >G22713 327 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 328 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 329 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 330 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCTG 331 | >G22608 332 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 333 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 334 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 335 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 336 | >G22712 337 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 338 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 339 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 340 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 341 | >G22569 342 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 343 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 344 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 345 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCCG 346 | >G22634 347 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAACCGATCATAC 348 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 349 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 350 | GCGGCCCCCGCTCTCCGGGGACGGTGCCTCGGTCTG 351 | >G22687 352 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 353 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 354 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 355 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 356 | >G22656 357 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 358 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 359 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 360 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 361 | >G22697 362 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 363 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGT 364 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 365 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 366 | >G22622 367 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 368 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 369 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 370 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 371 | >G22572 372 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 373 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 374 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 375 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 376 | >G22636 377 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAATCGATCATAC 378 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 379 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 380 | GCGGCCCCCGCTCTCCGGGAACGGTGCCTCGGTCTG 381 | >G22600 382 | CTCGTTCGGCGCGCCACGCTCGAAGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 383 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 384 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 385 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 386 | >G22611 387 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 388 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 389 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 390 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 391 | >G22632 392 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAATCGATCATAC 393 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 394 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 395 | GCGGCCCCCGCTCTCCGGGAACGGTGCCTCGGTTTG 396 | >G22633 397 | CTCGCTCCGCACGAGATGCTCGAGGCCCTGTCTTGCGAGCTCTGAGCGAATCGATCATAC 398 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 399 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 400 | GCGGCCCCCGCTCTCCGGGAACGGTGCCTCGGTTTG 401 | >G22586 402 | CTCGTTCGGCGCTCCACGTTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 403 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 404 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 405 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 406 | >G22727 407 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTAAGCGAACCGATCATGC 408 | TCGTTCCACCGCCCCAACCACCGTTACTCTCGCCAGAGAGCCCCCCGATCGGTCCGGCGC 409 | GCAGAGCGGGCCCTACGAGGGACTGCAATCAACACGGGCTTAATCGAGTGGCAGGGCCAT 410 | GCGGCCCTCGCGCTCTGGGGACGGCGCCCCGGTCCG 411 | >G22676 412 | CTCGCTCCGCGCGCCACGCTCGAGGCCCCGTCTTGCGGGCCCTGAGAGACCCGATCATAC 413 | TCGTCCCACCGCACTAACCACCGCCACCCTCGCCAGGGAACCCCCCGATCGGTCAGGCAC 414 | GCAGAGTGGGCCATACGCGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAC 415 | GCGGCCCTCGTTCTCCGGGGGCAGTGCCCGGGGCTG 416 | >G22660 417 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 418 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 419 | GCAAAGTGGGCCATACGCGGGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 420 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 421 | >G22679 422 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 423 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 424 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 425 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 426 | >G22648 427 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 428 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 429 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 430 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 431 | >G22631 432 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 433 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 434 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 435 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 436 | >G22575 437 | CTCGCTCCGCGCGCCCCGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 438 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 439 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 440 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 441 | >G22604 442 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 443 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 444 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 445 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 446 | >G22567 447 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 448 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACTCCCCGCCAGGTCAGGTAC 449 | ACAAAGTGGGCCATACGCGCGAAGATTGTCGACACAGGCTTAATTGGGTGGCGGGGTCAT 450 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 451 | >G22652 452 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 453 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 454 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 455 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 456 | >G22578 457 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 458 | CCGCCCCACAGCACCAACCANCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 459 | GCAGAATGGACCATCCTCAGGACTNCTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 460 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 461 | >G22706 462 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 463 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 464 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 465 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 466 | >G22624 467 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 468 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 469 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 470 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 471 | >G22675 472 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGTCTTGCGAGCTCTGAGCGAACCGATCATAC 473 | TTGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 474 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 475 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 476 | >G22617 477 | CTCGCTCCGCGCGCCCCGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 478 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 479 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 480 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 481 | >G22582 482 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 483 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 484 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 485 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 486 | >G22678 487 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGAGACCCGATCATAC 488 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 489 | GCAAAGTGGGCCATACGCGGGACTACTGTCGACAAGGACCGAATCGGGTGGCGGGGCCAT 490 | GCGGCCCTCACTCTCCGGGGACGGTGGCCGGGGCTG 491 | >G22649 492 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 493 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 494 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 495 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 496 | >G22645 497 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 498 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 499 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 500 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 501 | >G22621 502 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 503 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 504 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 505 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 506 | >G22717 507 | CTCGCTCCGAACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGACCGAACCGATCATGC 508 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 509 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGGGGCAGGGCCAT 510 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 511 | >G22566 512 | CTCGCTCCGCGTGCCACGCTCGCGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 513 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 514 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 515 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 516 | >G22654 517 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 518 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 519 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 520 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 521 | >G22571 522 | CTCGCTCCGAACGCGATACTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 523 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCTAGGGAGCCCCCCGATCGGTTCGGCGC 524 | GCAGAGCGTGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGGGGCAGGGCCAT 525 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 526 | >G22669 527 | CTCGTTCCACGCGCCACGCTCGAGGTCCCGTCTGAAGGGACCTGAGAGACCAAGCGGTAT 528 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAAGGAACCCCCCGCCCGGTCAGGTAC 529 | GCAAAGTGGGCCAGACGCGGGGATACTGTCGACACGGGATTCAATGGGTGACGGGGCCAT 530 | GCGGACCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 531 | >G22596 532 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 533 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 534 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 535 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 536 | >G22601 537 | CTCGCTCCGCGCGCCCCGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 538 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 539 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 540 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 541 | >G22651 542 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 543 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 544 | GCAGAATGGACNATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 545 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 546 | >G22662 547 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 548 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 549 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 550 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 551 | >G22591 552 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 553 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 554 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 555 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 556 | >G22599 557 | CTCGTTCGGCGCTCCACGTTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 558 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 559 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 560 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 561 | >G22589 562 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 563 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 564 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 565 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 566 | >G22722 567 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 568 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 569 | GCAAAGTGGGCCATACGCGGGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 570 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 571 | >G22610 572 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 573 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 574 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 575 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 576 | >G22707 577 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 578 | TCGTTCCACCGCACCCACCACCGCTACCCTCGTCAGGGAGCCCCCCGATCGATCCGGCGT 579 | GCCGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 580 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 581 | >G22703 582 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 583 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATATAC 584 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 585 | GCGGCTCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 586 | >G22640 587 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGTCTTGCGAGCTCTGAGCGAACCGATCATAC 588 | TTGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 589 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 590 | GCGGCCCCCGCTCTCCGGGGACGGTGCCCCGGTCTG 591 | >G22619 592 | CTCGCTCCGCGCGCCACGCTCGAGGCCCCGTCTTGCGGGCCCTGAGAGACCCGATCATAC 593 | TCGTCCCACCGCACTAACCACCGCCACCCTCGCCAGGGAACCCCCCGATCGGTCAGGCAC 594 | GCAGAGTGGGCCATACGCGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAC 595 | GCGGCCCTCGTTCTCCGGGGGCAGTGCCCGGGGCTG 596 | >G22629 597 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 598 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 599 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 600 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 601 | >G22695 602 | CTTGCTCCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 603 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCGGTCAGGTAC 604 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 605 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 606 | >G22688 607 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 608 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 609 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 610 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 611 | >G22593 612 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 613 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 614 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 615 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 616 | >G22581 617 | CTCGTTCGGCGCTCCACGNTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 618 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 619 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 620 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 621 | >G22705 622 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 623 | TCGTTCCACCGCACCCACCACCGCTACCCTCGTCAGGGAGCCCCCCGATCGATCCGGCGT 624 | GCCGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 625 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 626 | >G22616 627 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 628 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 629 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 630 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 631 | >G22587 632 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 633 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 634 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 635 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 636 | >G22639 637 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 638 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 639 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 640 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 641 | >G22650 642 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 643 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 644 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 645 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 646 | >G22655 647 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACTTGAGAGACCAAGCGGTAT 648 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 649 | GCAAAGTGGGGCATACGCGCNAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 650 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 651 | >G22692 652 | CTCGCGCCGCGCGCCACGCTCAAGGCCCCGTCTTGAGGACCCTGAGAGACCCGATCATAC 653 | TCGCCGCACCTGATCAACCACTGCCACCCGTGCCAGGGCACCCCCCGCCCGGTCAGGTAC 654 | GAAGAGTAGGCCATACGCGGGACTACTGTCGACCCGGGCTTAATCGGATGGCGGAGCCCT 655 | GTGTCCCTCGCTCCCCGGGGAAGGTGCCCGGGGCTG 656 | >G22665 657 | CTCGCTCCGCGCGCCCCGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 658 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 659 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 660 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 661 | >G22653 662 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 663 | TCGTTCCACCGCACCCACCACCGCTACCCTCGTCAGGGAGCCCCCCGATCGATCCGGCGT 664 | GCCGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 665 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 666 | >G22686 667 | TTTGCTGCGCGCGCCACGCTCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 668 | TCGCCCTGCCGCACCAACTACCGCCACCCTCGCCAGGGAACCCTCCGCCCAGTCAGGTAC 669 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCCAT 670 | GCGGCCCTCGCTTTTCGAGGACGGTACCCGGGGCTG 671 | >G22606 672 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACTTGAGAGACCAAGCGGTAT 673 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 674 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 675 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 676 | >G22628 677 | CTCGCTCCGCACGAGATGCTCGAGGCCCNGTCTTGCGAGCTCTGAGCGAACCGATCATAC 678 | TTGTTCCACCGCACCAACCACCGCTAACCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 679 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCACGGCCAT 680 | GCGGCCCCCGCTCTCCGGGNACGGTGCCNCGGTCTG 681 | >G22698 682 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 683 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATNTAC 684 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 685 | GCGGCTCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 686 | >G22702 687 | TTTGCTGCGCGCGCCACGCCCGAGACCCCGTCTGGAGGGCCCTGCGAGACCCGATCAGAC 688 | TCGCCCTGCCGCACCACCTACCGCCACCCTCGCCTGGGAACCCTCCGCCCAGTCAGGTAC 689 | GCAACGTGGGCCATACGCGGGACTACTGTGGCCACGGGCTTAATCGGGTAGCGGGGCTAT 690 | GCGGCCCTCGCTTTTCTAGGACGGTACCCGGGGCTG 691 | >G22626 692 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 693 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 694 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 695 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 696 | >G22691 697 | CTCGCGCCGCGCGCCACGCTCAAGGCCCCGTCTTGAGGACCCTGAGAGACCCGATCATAC 698 | TCGCCGCACCTGATCAACCANTGCCACCCGTGCCAGGGCACCCCCCGCCCGGTCAGGTAC 699 | GAAGAGTAGGCCATACGCGGGACTACTGTCGACCCGGGCTTAATCGGATGGCGGAGCCCT 700 | GTGTCCCTCGCTCCCCGGGGAAGGTGCCCGGGGCTG 701 | >G22613 702 | CTCGCTCCGCGCGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 703 | TCGCCCCACAGCACCAATCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 704 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 705 | GCAGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 706 | >G22585 707 | CTCGTTCGGCGCTCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 708 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCATGTAC 709 | GCAAAGTGGGCCATACGCGGGAATATTGTCGATACGGGCTTAATTGGGTGGCGGGGTCAT 710 | GCGGCTCTGGCTCTCCGGGGACGATGCCCGGGGCTG 711 | >G22701 712 | CTCGTTCGGCGCGCCACGCTCGAAGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 713 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACCCCCCGCCAGGTCAGGTAC 714 | GCAAAGTGGGCCATACGCGCGAATATTGTCGACACGGGCTTAATTGGGTGGCGGGGTCAT 715 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 716 | >G22565 717 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 718 | TCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCCCGCCCGGGCAGGTAC 719 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 720 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 721 | >G22671 722 | CTCGCTCCGCACGCGATGCTCGAGGCCCCGCCTTGCGAGCTCTGAGCGAACCGATCATGC 723 | TCGTTCCACCGCACCAACCACCGCTACCCTCGCCAGGGAGCCCCCCGATCGGTCCGGCGC 724 | GCAGAGCGGGCCATACGAGGGACTACAGTCAACACGGGCTTAATCGGGTGGCAGGGCCAT 725 | GCGGCCCTCGCTCTCCGGGGACGGTGCCCCGGTCTG 726 | >G22672 727 | CGCCCTCCGCGCGCCACGCTTGAGGCCCCGTGTGGAGGGCCCTGAGACACCCGATCATAC 728 | TCACCCCGCCGCACCAACTAGCGCCGCCCTCGCCAGGGAACCCTCCACCCGGTCAGGTAC 729 | GCAAAGTGGGCCATATGCGGGACTACTGTCGACAAGAACCGAATCGGGTGGCGGGGCCAT 730 | ACGGCCCTCACTCTCCGGAGACGGTGGCCGGGGCTG 731 | >G22620 732 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 733 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 734 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 735 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 736 | >G22659 737 | CTCGCTCCGCGTGCCACGCTCGAGGCATCGTCCTGAAGGCCCGGAGAGGCCCGATCATAC 738 | CCGCCCCACAGCACCAACCACCACCACCCTCACCAGGAAATCCCTCGCCCGGGCAGGTAC 739 | GCAGAATGGACCATCCTCAGGACTACTGCCGACACGGGCTTACTCAGGTGGCGGGACCAT 740 | GCGGCCTTCGCTCTCCGGGGACGGTGCGCGAGGCTC 741 | >G22573 742 | CTCGTTCGGCGCGCCACGCTCGAGGCCCCATCTGAAGGGACCTGAGAGACCAAGCGGTAT 743 | TCGCCCCGACGCACCAACCGCCGCCACCATCGCCAGGGAACTCCCCGCCAGGTCAGGTAC 744 | ACAAAGTGGGCCATACGCGCGAAGATTGTCGACACAGGCTTAATTGGGTGGCGGGGTCAT 745 | GCGGCCCTGGCTCTCCGGGGACGGTGCCCGGGGCTG 746 | -------------------------------------------------------------------------------- /data/tb/lee_2015.metadata.tsv: -------------------------------------------------------------------------------- 1 | strain accession date region country location db authors cluster paper_url title 2 | G22670 10155 1991-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 3 | G22671 10223 1992-XX-XX north_america canada village_d genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 4 | G22672 11011 1991-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 5 | G22673 11234 1992-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 6 | G22674 14069 1993-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 7 | G22675 14508 1993-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 8 | G22676 15613 1994-XX-XX north_america canada village_e genbank Lee et al Mj-V.d http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 9 | G22677 16490 1995-XX-XX north_america canada village_e genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 10 | G22678 16493 1995-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 11 | G22679 18421 1996-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 12 | G22680 18422 1996-XX-XX north_america canada village_k genbank Lee et al Mj-I http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 13 | G22681 18747 1996-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 14 | G22682 18988 1996-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 15 | G22683 19057 1996-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 16 | G22684 19276 1996-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 17 | G22685 50045 1996-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 18 | G22686 50179 1997-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 19 | G22687 50248 1997-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 20 | G22688 53221 1998-XX-XX north_america canada village_c genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 21 | G22689 54902 1999-XX-XX north_america canada other_village genbank Lee et al Mj-IV.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 22 | G22690 55546 2000-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 23 | G22691 55753 2000-XX-XX north_america canada village_b genbank Lee et al Mj-VI http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 24 | G22692 55988 2005-XX-XX north_america canada village_b genbank Lee et al Mj-VI http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 25 | G22693 55989 2000-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 26 | G22694 56828 2000-XX-XX north_america canada other_village genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 27 | G22695 57052 2001-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 28 | G22696 58385 2001-XX-XX north_america canada other_village genbank Lee et al NA http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 29 | G22697 60053 2002-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 30 | G22698 62796 2004-XX-XX north_america canada village_e genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 31 | G22699 62806 2004-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 32 | G22700 62957 2004-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 33 | G22701 63113 2004-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 34 | G22702 63670 2004-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 35 | G22703 63878 2004-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 36 | G22704 64165 2004-XX-XX north_america canada village_k genbank Lee et al Mj-II http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 37 | G22705 64334 2005-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 38 | G22706 64712 2005-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 39 | G22707 65165 2005-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 40 | G22708 66591 2006-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 41 | G22709 68995 2007-XX-XX north_america canada village_k genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 42 | G22710 73787 2010-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 43 | G22711 74856 2010-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 44 | G22712 78932 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 45 | G22713 79031 2012-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 46 | G22669 9965 1991-XX-XX north_america canada village_d genbank Lee et al Mj-IV.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 47 | G22589 MT-0080 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 48 | G22668 MT-0712 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 49 | G22582 MT-0718 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 50 | G22587 MT-0972 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 51 | G22590 MT-1103 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 52 | G22591 MT-1128 2011-XX-XX north_america canada village_b genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 53 | G22592 MT-1167 2008-XX-XX north_america canada village_b genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 54 | G22593 MT-1206 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 55 | G22666 MT-1212 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 56 | G22594 MT-1247 2012-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 57 | G22714 MT-13-1408 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 58 | G22715 MT-13-1711 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 59 | G22716 MT-13-1712 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 60 | G22717 MT-13-1753 2013-XX-XX north_america canada village_a genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 61 | G22718 MT-13-1828 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 62 | G22719 MT-13-1835 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 63 | G22720 MT-13-1892 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 64 | G22721 MT-13-2012 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 65 | G22722 MT-13-2334 2013-XX-XX north_america canada village_a genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 66 | G22723 MT-13-2384 2013-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 67 | G22725 MT-13-2690 2013-XX-XX north_america canada village_a genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 68 | G22726 MT-13-2761 2013-XX-XX north_america canada village_a genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 69 | G22727 MT-13-3209 2013-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 70 | G22728 MT-13-848 2013-XX-XX north_america canada village_a genbank Lee et al Mn http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 71 | G22595 MT-131 2011-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 72 | G22596 MT-1336 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 73 | G22597 MT-1345 2011-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 74 | G22598 MT-1393 2008-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 75 | G22599 MT-140 2009-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 76 | G22600 MT-1403 2009-XX-XX north_america canada village_e genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 77 | G22601 MT-1466 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 78 | G22602 MT-1499 2011-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 79 | G22603 MT-1549 2008-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 80 | G22604 MT-1605 2008-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 81 | G22605 MT-1684 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 82 | G22606 MT-1799 2011-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 83 | G22607 MT-1838 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 84 | G22608 MT-1971 2011-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 85 | G22609 MT-2151 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 86 | G22610 MT-2174 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 87 | G22611 MT-2175 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 88 | G22612 MT-2178 2011-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 89 | G22613 MT-2184 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 90 | G22614 MT-2224 2008-XX-XX north_america canada village_e genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 91 | G22615 MT-2356 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 92 | G22616 MT-2465 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 93 | G22617 MT-2473 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 94 | G22618 MT-2474 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 95 | G22619 MT-2538 2011-XX-XX north_america canada village_c genbank Lee et al Mj-V.d http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 96 | G22620 MT-2665 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 97 | G22621 MT-2667 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 98 | G22622 MT-2706 2010-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 99 | G22623 MT-2720 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 100 | G22624 MT-2762 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 101 | G22625 MT-2768 2009-XX-XX north_america canada village_e genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 102 | G22626 MT-2769 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 103 | G22627 MT-2771 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 104 | G22628 MT-2792 2006-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 105 | G22629 MT-2800 2010-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 106 | G22631 MT-289 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 107 | G22632 MT-2905 2006-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 108 | G22633 MT-2910 2006-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 109 | G22634 MT-2931 2006-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 110 | G22635 MT-3000 2009-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 111 | G22636 MT-3004 2009-XX-XX north_america canada village_c genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 112 | G22637 MT-3074 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 113 | G22638 MT-3173 2009-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 114 | G22639 MT-3194 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 115 | G22640 MT-3239 2006-XX-XX north_america canada other_village genbank Lee et al Mj-V.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 116 | G22641 MT-3255 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 117 | G22642 MT-3271 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 118 | G22643 MT-3281 2010-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 119 | G22644 MT-3296 2011-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 120 | G22645 MT-3341 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 121 | G22648 MT-3673 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 122 | G22649 MT-3683 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 123 | G22651 MT-3787 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 124 | G22652 MT-389 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 125 | G22653 MT-393 2009-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 126 | G22729 MT-398 2005-XX-XX north_america canada other_village genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 127 | G22654 MT-405 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 128 | G22655 MT-4067 2007-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 129 | G22656 MT-4137 2010-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 130 | G22667 MT-4166 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 131 | G22730 MT-4230 2010-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 132 | G22657 MT-441 2011-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 133 | G22731 MT-4466 2011-XX-XX north_america canada village_d genbank Lee et al Mj-IV.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 134 | G22658 MT-452 2011-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 135 | G22659 MT-467 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 136 | G22660 MT-4683 2011-XX-XX north_america canada village_d genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 137 | G22661 MT-4846 2011-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 138 | G22662 MT-4854 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 139 | G22663 MT-4884 2011-XX-XX north_america canada village_c genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 140 | G22664 MT-4942 2007-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 141 | G22665 MT-504 2011-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 142 | G22565 MT-5195 2007-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 143 | G22566 MT-5337 2007-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 144 | G22567 MT-5373 2009-XX-XX north_america canada other_village genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 145 | G22568 MT-5383 2007-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 146 | G22569 MT-5447 2011-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 147 | G22732 MT-5488 2007-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 148 | G22570 MT-5531 2011-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 149 | G22571 MT-5543 2007-XX-XX north_america canada village_k genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 150 | G22572 MT-567 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 151 | G22733 MT-578 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 152 | G22573 MT-5870 2009-XX-XX north_america canada other_village genbank Lee et al Mj-IV.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 153 | G22574 MT-5983 2011-XX-XX north_america canada village_k genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 154 | G22575 MT-6084 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 155 | G22576 MT-6205 2011-XX-XX north_america canada village_a genbank Lee et al Mj-V.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 156 | G22577 MT-6218 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 157 | G22578 MT-6226 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 158 | G22579 MT-6429 2012-XX-XX north_america canada village_k genbank Lee et al Mj-III.b http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 159 | G22580 MT-661 2009-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 160 | G22581 MT-692 2009-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 161 | G22583 MT-721 2008-XX-XX north_america canada village_a genbank Lee et al Mj-III.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 162 | G22584 MT-751 2008-XX-XX north_america canada village_b genbank Lee et al Mj-V.a http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 163 | G22585 MT-853 2011-XX-XX north_america canada village_c genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 164 | G22586 MT-877 2010-XX-XX north_america canada other_village genbank Lee et al Mj-IV.c http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 165 | G22650 None1 20XX-XX-XX north_america canada genbank Lee et al http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 166 | G22724 None2 20XX-XX-XX north_america canada genbank Lee et al http://www.pnas.org/content/112/44/13609 Population_Genomics_of_Mycobacterium_tuberculosis_in_the_Inuit 167 | -------------------------------------------------------------------------------- /data/tb/lee_2015.nwk: -------------------------------------------------------------------------------- 1 | (G22644:0.00000100,((((((((((((((((((((G22725:0.00000100,G22726:0.00000100):0.00696507,G22655:0.00000213):0.00696459,G22606:0.00000213):0.00462521,(G22567:0.00000100,G22573:0.00000100):0.01870812):0.00000217,((((G22699:0.00000000,G22701:0.00000000):0.00000000,G22724:0.00000000):0.00000000,G22600:0.00000000):0.00000100,G22700:0.00000100):0.00462806):0.00000231,((G22687:0.00000000,G22650:0.00000000):0.00000000,G22688:0.00000000):0.00000213):0.00000196,G22706:0.00000213):0.00000233,G22685:0.00000227):0.00464036,((G22677:0.00000000,G22722:0.00000000):0.00000213,G22660:0.00000213):0.00000280):0.00000294,((((((G22657:0.00000000,G22585:0.00000000):0.00000000,G22658:0.00000000):0.00000000,G22608:0.00000000):0.00000213,G22602:0.00000100):0.00000287,(G22580:0.00000213,((G22586:0.00000100,G22599:0.00000100):0.00000207,G22581:0.00000100):0.00444218):0.00011835):0.00457355,(((G22625:0.00000100,G22703:0.00000100):0.00457201,G22698:0.00000213):0.00000209,G22614:0.00000213):0.00000278):0.01869776):0.02220554,(G22689:0.00000100,G22669:0.00000100):0.05133894):0.08609436,(((((((G22684:0.00000000,G22686:0.00000000):0.00000000,G22682:0.00000000):0.00000000,G22681:0.00000000):0.00000213,G22683:0.00000100):0.00000270,(G22704:0.00000100,G22702:0.00000100):0.02379237):0.01411310,G22695:0.00000213):0.06649782,((((((G22670:0.00000000,G22673:0.00000000):0.00000000,G22672:0.00000000):0.00000000,G22679:0.00000000):0.00000000,G22680:0.00000000):0.00000100,G22674:0.00000100):0.02378897,G22678:0.00000213):0.07247964):0.00726436):0.01537637,(G22692:0.00000213,G22691:0.00000287):0.10913650):0.00000265,(((((((((((((((((G22583:0.00000000,G22565:0.00000000):0.00000000,G22568:0.00000000):0.00000000,G22711:0.00000000):0.00000000,G22667:0.00000000):0.00000000,G22664:0.00000000):0.00000000,G22648:0.00000000):0.00000000,G22627:0.00000000):0.00000000,G22622:0.00000000):0.00000000,G22645:0.00000000):0.00000000,G22712:0.00000000):0.00000000,G22629:0.00000000):0.00000000,G22623:0.00000000):0.00000000,G22732:0.00000000):0.00000213,G22637:0.00000100):0.00000205,(G22574:0.00000100,G22566:0.00000100):0.00467145):0.00000207,((((((((((((((((((((G22733:0.00000000,G22610:0.00000000):0.00000000,G22590:0.00000000):0.00000000,G22626:0.00000000):0.00000000,G22620:0.00000000):0.00000000,G22589:0.00000000):0.00000000,G22607:0.00000000):0.00000000,G22659:0.00000000):0.00000000,G22609:0.00000000):0.00000000,G22591:0.00000000):0.00000000,G22582:0.00000000):0.00000000,G22587:0.00000000):0.00000000,G22621:0.00000000):0.00000000,G22572:0.00000000):0.00000000,G22652:0.00000000):0.00000000,G22577:0.00000000):0.00000000,G22631:0.00000000):0.00000000,G22654:0.00000000):0.00000213,G22668:0.00000100):0.00000211,G22651:0.00000213):0.00000224,G22578:0.00000238):0.00933016):0.00465947,((((((((((((((((G22642:0.00000000,G22613:0.00000000):0.00000000,G22662:0.00000000):0.00000000,G22593:0.00000000):0.00000000,G22616:0.00000000):0.00000000,G22596:0.00000000):0.00000000,G22618:0.00000000):0.00000000,G22710:0.00000000):0.00000000,G22666:0.00000000):0.00000000,G22624:0.00000000):0.00000000,G22579:0.00000000):0.00000000,G22638:0.00000000):0.00000000,G22649:0.00000000):0.00000000,G22639:0.00000000):0.00000213,G22605:0.00000100):0.00000298,((((G22615:0.00000000,G22665:0.00000000):0.00000000,G22617:0.00000000):0.00000000,G22601:0.00000000):0.00000100,G22575:0.00000100):0.00466263):0.00933596,(((G22603:0.00000000,G22604:0.00000000):0.00000000,G22611:0.00000000):0.00000213,G22598:0.00000100):0.00000205):0.00000247):0.13054101):0.04177716,(G22676:0.00000100,G22619:0.00000100):0.02250563):0.08431666,(((((((G22635:0.00000000,G22636:0.00000000):0.00000213,G22708:0.00000100):0.00000218,(G22632:0.00000100,G22633:0.00000100):0.00458634):0.00923292,G22628:0.00000213):0.00000236,G22634:0.00000213):0.02364251,G22640:0.00000213):0.00465688,G22675:0.00000213):0.00393954):0.01013712,(((((G22592:0.00000263,(G22584:0.00000213,G22717:0.00000100):0.00000263):0.00471774,(G22709:0.00000100,G22571:0.00000100):0.01890108):0.00471777,G22663:0.00000213):0.00469569,(G22690:0.00000100,G22693:0.00000100):0.01407471):0.00000215,(G22656:0.00000213,G22671:0.00000100):0.00000206):0.00000208):0.00000214,((((G22723:0.00000100,G22727:0.00000100):0.00468532,(G22576:0.00000213,G22569:0.00000100):0.00000243):0.00000214,G22595:0.00000213):0.00468022,(((G22612:0.00000000,G22713:0.00000000):0.00000000,G22643:0.00000000):0.00000100,G22730:0.00000100):0.00000282):0.05349733):0.00468000,G22697:0.00000213):0.01895884,((G22707:0.00000000,G22653:0.00000000):0.00000213,G22705:0.00000100):0.00000220):0.00466455,G22597:0.00000100):0.00000000; 2 | -------------------------------------------------------------------------------- /data/tb/lee_2015.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/data/tb/lee_2015.vcf.gz -------------------------------------------------------------------------------- /data/zika/zika.country_weights.csv: -------------------------------------------------------------------------------- 1 | #country,weight 2 | american_samoa,55 3 | brazil,200000 4 | china,1000000 5 | colombia,50000 6 | cuba,12000 7 | dominican_republic,10000 8 | ecuador,16000 9 | french_guiana,280 10 | french_polynesia,276 11 | guadeloupe,400 12 | guatemala,17000 13 | haiti,10000 14 | honduras,9000 15 | martinique,385 16 | mexico,124000 17 | panama,4000 18 | puerto_rico,3400 19 | suriname,558 -------------------------------------------------------------------------------- /data/zika/zika.metadata.csv: -------------------------------------------------------------------------------- 1 | #name,date,country 2 | PuertoRico/ZF8/2016|PuertoRico/ZF8/2016|2016-06-13|puerto_rico,2016-06-13,puerto_rico 3 | PRVABC59|KX601168|2015-12-01|puerto_rico,2015-12-01,puerto_rico 4 | Martinique/ZF1/2016|Martinique/ZF1/2016|2016-03-07|martinique,2016-03-07,martinique 5 | NL00013|KU937936|2016-02-11|suriname,2016-02-11,suriname 6 | V17271|KU758877|2015-12-15|french_guiana,2015-12-15,french_guiana 7 | BeH819015|KU365778|2015-07-01|brazil,2015-07-01,brazil 8 | GZ01|KU820898|2016-02-14|china,2016-02-14,china 9 | GD01|KU740184|2016-02-15|china,2016-02-15,china 10 | GDZ16001|KU761564|2016-02-12|china,2016-02-12,china 11 | Z16019|KU955590|2016-02-26|china,2016-02-26,china 12 | GZ02/2016|KX056898|2016-02-25|china,2016-02-25,china 13 | Z1106033|KU312312|2015-10-02|suriname,2015-10-02,suriname 14 | BeH815744|KU365780|2015-07-01|brazil,2015-07-01,brazil 15 | BeH818995|KU365777|2015-07-01|brazil,2015-07-01,brazil 16 | BeH819966|KU365779|2015-07-01|brazil,2015-07-01,brazil 17 | SSABR1|KU707826|2015-07-01|brazil,2015-07-01,brazil 18 | Aedessp/MEX/MEX_2_81/2016|KX446950|2016-01-01|mexico,2016-01-01,mexico 19 | Aedessp/MEX/MEX_I_7/2016|KX446951|2016-01-01|mexico,2016-01-01,mexico 20 | MEX_I_7|KX247632|2015-11-15|mexico,2015-11-15,mexico 21 | FB_GWUH_2016|KU870645|2016-02-02|guatemala,2016-02-02,guatemala 22 | V103344|KU501216|2015-12-01|guatemala,2015-12-01,guatemala 23 | V8375|KU501217|2015-11-01|guatemala,2015-11-01,guatemala 24 | HND/R103451/2015|KX694534|2016-07-01|honduras,2016-07-01,honduras 25 | V103451|KX262887|2016-01-06|honduras,2016-01-06,honduras 26 | Rio_U1|KU926309|2016-01-14|brazil,2016-01-14,brazil 27 | PAN/CDC_259249_V1_V3/2015|KX156775|2015-12-11|panama,2015-12-11,panama 28 | PAN/CDC_259359_V1_V3/2015|KX156774|2015-12-18|panama,2015-12-18,panama 29 | PAN/CDC_259364_V1_V2/2015|KX156776|2015-12-18|panama,2015-12-18,panama 30 | FLR|KU820897|2015-12-15|colombia,2015-12-15,colombia 31 | COL/FLR/2015|KX087102|2015-12-15|colombia,2015-12-15,colombia 32 | COL/UF_1/2016|KX247646|2016-02-09|colombia,2016-02-09,colombia 33 | PAN/BEI_259634_V4/2016|KX198135|2016-07-01|panama,2016-07-01,panama 34 | COL/FCC00093/2015|KX548902|2015-10-07|colombia,2015-10-07,colombia 35 | MEX/InDRE/Sm/2016|KU922960|2016-02-25|mexico,2016-02-25,mexico 36 | MRS_OPY_Martinique_PaRi_2015|KU647676|2015-12-15|martinique,2015-12-15,martinique 37 | Brazil/PE243/2015|KX197192|2015-07-01|brazil,2015-07-01,brazil 38 | SPH2015|KU321639|2015-03-15|brazil,2015-03-15,brazil 39 | Haiti/1225/2014|KU509998|2014-12-12|haiti,2014-12-12,haiti 40 | Haiti/1/2016|KX051563|2016-02-05|haiti,2016-02-05,haiti 41 | Brazil_ZKV2015|KU497555|2015-11-30|brazil,2015-11-30,brazil 42 | Brazil/2016/INMI1|KU991811|2016-03-06|brazil,2016-03-06,brazil 43 | PHE_semen_Guadeloupe|KX673530|2016-04-21|guadeloupe,2016-04-21,guadeloupe 44 | Cuba/ZF10/2016|Cuba/ZF10/2016|2016-06-02|cuba,2016-06-02,cuba 45 | Dominican_Republic/2016/PD1|KU853012|2016-02-01|dominican_republic,2016-02-01,dominican_republic 46 | BeH823339|KU729217|2015-07-01|brazil,2015-07-01,brazil 47 | Rio_S1|KU926310|2016-01-29|brazil,2016-01-29,brazil 48 | Natal_RGN|KU527068|2015-07-01|brazil,2015-07-01,brazil 49 | Ecuador/EC062/2016|Ecuador/EC062/2016|2016-04-15|ecuador,2016-04-15,ecuador 50 | Ecuador/EC089/2016|Ecuador/EC089/2016|2016-04-15|ecuador,2016-04-15,ecuador 51 | Paraiba_01|KX280026|2015-07-01|brazil,2015-07-01,brazil 52 | Bahia04|KX101062|2015-06-15|brazil,2015-06-15,brazil 53 | Bahia08|KU940227|2015-07-15|brazil,2015-07-15,brazil 54 | Bahia05|KX101063|2015-12-15|brazil,2015-12-15,brazil 55 | HS_2015_BA_01|KX520666|2015-07-01|brazil,2015-07-01,brazil 56 | Bahia09|KU940224|2015-08-01|brazil,2015-08-01,brazil 57 | Bahia12|KX101067|2015-05-15|brazil,2015-05-15,brazil 58 | Bahia07|KU940228|2015-07-01|brazil,2015-07-01,brazil 59 | Bahia03|KX101061|2015-05-15|brazil,2015-05-15,brazil 60 | Bahia11|KX101064|2015-04-15|brazil,2015-04-15,brazil 61 | Bahia15|KX101065|2016-01-15|brazil,2016-01-15,brazil 62 | Bahia01|KX101066|2015-05-15|brazil,2015-05-15,brazil 63 | Bahia02|KX101060|2015-05-15|brazil,2015-05-15,brazil 64 | BeH828305|KU729218|2015-07-01|brazil,2015-07-01,brazil 65 | 1_0049_PF|KX447510|2013-12-15|french_polynesia,2013-12-15,french_polynesia 66 | 1_0117_PF|KX447518|2013-12-15|french_polynesia,2013-12-15,french_polynesia 67 | 1_0016_PF|KX447520|2014-01-15|french_polynesia,2014-01-15,french_polynesia 68 | PF13/251013_18|KX369547|2013-10-25|french_polynesia,2013-10-25,french_polynesia 69 | 1_0181_PF|KX447512|2013-12-15|french_polynesia,2013-12-15,french_polynesia 70 | 1_0134_PF|KX447513|2013-12-15|french_polynesia,2013-12-15,french_polynesia 71 | 1_0199_PF|KX447519|2013-11-15|french_polynesia,2013-11-15,french_polynesia 72 | 1_0015_PF|KX447511|2014-01-15|french_polynesia,2014-01-15,french_polynesia 73 | SZ01/2016/China|KU866423|2016-07-01|american_samoa,2016-07-01,american_samoa 74 | Zhejiang04|KX117076|2016-02-17|china,2016-02-17,china 75 | SZ_WIV01|KU963796|2016-07-01|american_samoa,2016-07-01,american_samoa 76 | ZJ03|KU820899|2016-02-17|china,2016-02-17,china 77 | CN/SZ02/2016|KX185891|2016-02-17|american_samoa,2016-02-17,american_samoa 78 | ZKC2/2016|KX253996|2016-02-16|china,2016-02-16,china 79 | Z16006|KU955589|2016-02-16|china,2016-02-16,china 80 | SMGC_1|KX266255|2016-02-14|china,2016-02-14,china 81 | 1_0035_PF|KX447514|2014-01-15|french_polynesia,2014-01-15,french_polynesia 82 | 1_0080_PF|KX447521|2014-02-15|french_polynesia,2014-02-15,french_polynesia 83 | H/PF/2013|KJ776791|2013-11-28|french_polynesia,2013-11-28,french_polynesia 84 | 1_0087_PF|KX447509|2013-12-15|french_polynesia,2013-12-15,french_polynesia 85 | 1_0111_PF|KX447516|2014-01-15|french_polynesia,2014-01-15,french_polynesia 86 | 1_0030_PF|KX447515|2013-11-15|french_polynesia,2013-11-15,french_polynesia 87 | 1_0038_PF|KX447517|2014-01-15|french_polynesia,2014-01-15,french_polynesia 88 | -------------------------------------------------------------------------------- /data/zika/zika.nwk: -------------------------------------------------------------------------------- 1 | (((((((((((('PuertoRico/ZF8/2016|PuertoRico/ZF8/2016|2016-06-13|puerto_rico':0.00087,'PRVABC59|KX601168|2015-12-01|puerto_rico':0.0):0.00028,'Martinique/ZF1/2016|Martinique/ZF1/2016|2016-03-07|martinique':0.00068):0.00095,('NL00013|KU937936|2016-02-11|suriname':0.00096,'V17271|KU758877|2015-12-15|french_guiana':0.00058):0.00019,'BeH819015|KU365778|2015-07-01|brazil':0.00113):0.00019,(('GZ01|KU820898|2016-02-14|china':0.00023,('GD01|KU740184|2016-02-15|china':0.0,'GDZ16001|KU761564|2016-02-12|china':0.0):0.00015):0.00067,('Z16019|KU955590|2016-02-26|china':0.00019,'GZ02/2016|KX056898|2016-02-25|china':0.0):0.00073):0.00109):9e-05,'Z1106033|KU312312|2015-10-02|suriname':0.00127):0.00019,(('BeH815744|KU365780|2015-07-01|brazil':0.00019,'BeH818995|KU365777|2015-07-01|brazil':0.0):0.00038,'BeH819966|KU365779|2015-07-01|brazil':0.0,'SSABR1|KU707826|2015-07-01|brazil':0.0):0.00085):0.00047,((('Aedessp/MEX/MEX_2_81/2016|KX446950|2016-01-01|mexico':0.00056,('Aedessp/MEX/MEX_I_7/2016|KX446951|2016-01-01|mexico':0.00019,'MEX_I_7|KX247632|2015-11-15|mexico':0.0):0.00037):0.00075,'FB_GWUH_2016|KU870645|2016-02-02|guatemala':0.00178,('V103344|KU501216|2015-12-01|guatemala':0.0001,'V8375|KU501217|2015-11-01|guatemala':0.0):0.00088,('HND/R103451/2015|KX694534|2016-07-01|honduras':0.00028,'V103451|KX262887|2016-01-06|honduras':9e-05):0.00047):0.00075,'Rio_U1|KU926309|2016-01-14|brazil':0.00141):9e-05):9e-05,(((((('PAN/CDC_259249_V1_V3/2015|KX156775|2015-12-11|panama':0.00028,'PAN/CDC_259359_V1_V3/2015|KX156774|2015-12-18|panama':0.00024,'PAN/CDC_259364_V1_V2/2015|KX156776|2015-12-18|panama':9e-05):0.00061,(('FLR|KU820897|2015-12-15|colombia':0.0,'COL/FLR/2015|KX087102|2015-12-15|colombia':0.0):0.00022,'COL/UF_1/2016|KX247646|2016-02-09|colombia':0.00015):0.00056):0.00018,'PAN/BEI_259634_V4/2016|KX198135|2016-07-01|panama':0.00057):0.00019,('COL/FCC00093/2015|KX548902|2015-10-07|colombia':0.00124,('MEX/InDRE/Sm/2016|KU922960|2016-02-25|mexico':0.00038,'MRS_OPY_Martinique_PaRi_2015|KU647676|2015-12-15|martinique':0.0):0.00067):0.0001):0.0008,((('Brazil/PE243/2015|KX197192|2015-07-01|brazil':0.00093,'SPH2015|KU321639|2015-03-15|brazil':0.0):0.00046,'Haiti/1225/2014|KU509998|2014-12-12|haiti':0.0):0.00028,'Haiti/1/2016|KX051563|2016-02-05|haiti':0.00075):0.00075):0.00027,('Brazil_ZKV2015|KU497555|2015-11-30|brazil':0.00212,'Brazil/2016/INMI1|KU991811|2016-03-06|brazil':0.00095):0.00017):0.00049,((((('PHE_semen_Guadeloupe|KX673530|2016-04-21|guadeloupe':0.00114,'Cuba/ZF10/2016|Cuba/ZF10/2016|2016-06-02|cuba':0.00087):9e-05,'Dominican_Republic/2016/PD1|KU853012|2016-02-01|dominican_republic':0.00048):0.00133,'BeH823339|KU729217|2015-07-01|brazil':0.00144):0.00018,('Rio_S1|KU926310|2016-01-29|brazil':0.00188,'Natal_RGN|KU527068|2015-07-01|brazil':0.00159):9e-05):9e-05,(('Ecuador/EC062/2016|Ecuador/EC062/2016|2016-04-15|ecuador':0.0002,'Ecuador/EC089/2016|Ecuador/EC089/2016|2016-04-15|ecuador':0.0001):0.00134,'Paraiba_01|KX280026|2015-07-01|brazil':0.00084):9e-05):0.00019,(((((('Bahia04|KX101062|2015-06-15|brazil':0.00068,'Bahia08|KU940227|2015-07-15|brazil':0.0,'Bahia05|KX101063|2015-12-15|brazil':0.0):0.00033,(('HS_2015_BA_01|KX520666|2015-07-01|brazil':0.00048,'Bahia09|KU940224|2015-08-01|brazil':0.0):0.00016,'Bahia12|KX101067|2015-05-15|brazil':0.0,'Bahia07|KU940228|2015-07-01|brazil':0.0):0.00016,'Bahia03|KX101061|2015-05-15|brazil':0.00067):0.00021,'Bahia11|KX101064|2015-04-15|brazil':0.00029,'Bahia15|KX101065|2016-01-15|brazil':0.0):0.00021,'Bahia01|KX101066|2015-05-15|brazil':0.00115):0.00026,'Bahia02|KX101060|2015-05-15|brazil':0.00046):0.00115,'BeH828305|KU729218|2015-07-01|brazil':0.00123):9e-05):0.00037,'1_0049_PF|KX447510|2013-12-15|french_polynesia':0.00038,'1_0117_PF|KX447518|2013-12-15|french_polynesia':0.00033):0.00028,'1_0016_PF|KX447520|2014-01-15|french_polynesia':0.00102,('PF13/251013_18|KX369547|2013-10-25|french_polynesia':0.00056,'1_0181_PF|KX447512|2013-12-15|french_polynesia':0.00019):9e-05,('1_0134_PF|KX447513|2013-12-15|french_polynesia':0.00038,'1_0199_PF|KX447519|2013-11-15|french_polynesia':0.00011):9e-05,'1_0015_PF|KX447511|2014-01-15|french_polynesia':0.00057):9e-05,(('SZ01/2016/China|KU866423|2016-07-01|american_samoa':0.0002,'Zhejiang04|KX117076|2016-02-17|china':0.00019,'SZ_WIV01|KU963796|2016-07-01|american_samoa':0.00019,'ZJ03|KU820899|2016-02-17|china':9e-05,'CN/SZ02/2016|KX185891|2016-02-17|american_samoa':0.0):0.00047,('ZKC2/2016|KX253996|2016-02-16|china':0.0,'Z16006|KU955589|2016-02-16|china':0.0,'SMGC_1|KX266255|2016-02-14|china':0.0):0.00018):0.00235,('1_0035_PF|KX447514|2014-01-15|french_polynesia':0.00048,'1_0080_PF|KX447521|2014-02-15|french_polynesia':0.00047,'H/PF/2013|KJ776791|2013-11-28|french_polynesia':0.00028,'1_0087_PF|KX447509|2013-12-15|french_polynesia':0.00019):9e-05,'1_0111_PF|KX447516|2014-01-15|french_polynesia':0.00066,'1_0030_PF|KX447515|2013-11-15|french_polynesia':0.00048):0.00015,'1_0038_PF|KX447517|2014-01-15|french_polynesia':0.00118):0.001; 2 | -------------------------------------------------------------------------------- /figures/clock_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/figures/clock_plot.png -------------------------------------------------------------------------------- /figures/ebola_outliers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/figures/ebola_outliers.png -------------------------------------------------------------------------------- /figures/ebola_skyline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/figures/ebola_skyline.png -------------------------------------------------------------------------------- /figures/timetree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/figures/timetree.png -------------------------------------------------------------------------------- /figures/tree_and_clock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neherlab/treetime_examples/260e7150c5edcb9d5b6394ee2798e2ce1043bf76/figures/tree_and_clock.png -------------------------------------------------------------------------------- /scripts/ancestral_sequence_inference.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function, division 2 | import numpy as np 3 | from Bio import Phylo 4 | import matplotlib.pyplot as plt 5 | from treetime import TreeAnc 6 | import treetime 7 | 8 | if __name__ == '__main__': 9 | plt.ion() 10 | 11 | # path to data 12 | base_name = '../data/h3n2_na/h3n2_na_200' 13 | 14 | # instantiate treetime 15 | myTree = TreeAnc(gtr='Jukes-Cantor', tree=base_name+".nwk", aln=base_name+'.fasta', verbose = 0) 16 | 17 | # infer a GTR model and ML ancestral sequences, either marginally or jointly most likely 18 | myTree.infer_ancestral_sequences(infer_gtr=True, marginal=True) 19 | 20 | # lets examine the properties of a node in the tree after ancestral inference 21 | node = myTree.tree.get_nonterminals()[7] 22 | # each node now has an inferred sequence 23 | if treetime.version<"0.7": 24 | print("\nthe inferred sequences is an array of characters:", node.sequence) 25 | else: 26 | print("\nthe inferred sequences is an array of characters:", myTree.sequence(node, as_string=False)) 27 | 28 | # in addition, each node of the tree now has an mutation object attached 29 | # note that the mutation numbering starts at 0 rather than 1 30 | print("\nmutations on the branch leading to node %s:"%node.name, node.mutations) 31 | 32 | # we can readily verify these mutations by checking the inferred sequences 33 | if node.mutations: 34 | mut = node.mutations[0] 35 | if treetime.version<"0.7": 36 | print("\nmutation %s%d%s corresponds to"%mut, 37 | "parent state: %s, child state %s\n\n"%(node.up.sequence[mut[1]], node.sequence[mut[1]])) 38 | else: 39 | print("\nmutation %s%d%s corresponds to"%mut, 40 | "parent state: %s, child state %s\n\n"%(myTree.sequence(node.up)[mut[1]], myTree.sequence(node)[mut[1]])) 41 | 42 | 43 | # plot the tree and label branches by mutation 44 | fig, ax = plt.subplots(1,1,figsize=(18,13)) 45 | ax.set_title("branches annotated by inferred mutations", fontsize=18) 46 | ax.set_axis_off() 47 | Phylo.draw(myTree.tree, label_func = lambda x:"", axes=ax, 48 | branch_labels=lambda x:", ".join(map(lambda m: "%s%d%s"%m, x.mutations[:3])) 49 | +('...' if len(x.mutations)>3 else "")) 50 | 51 | # finally, we print the inferred GTR model 52 | print(myTree.gtr) 53 | -------------------------------------------------------------------------------- /scripts/ebola.py: -------------------------------------------------------------------------------- 1 | ''' 2 | this script illustrates the use of treetime to analyze viral sequences. 3 | As an example, we use Ebola virus sequences from the 2014-2015 outbreak in 4 | West Africa. This example contains more than 300 sequences, it will take 5 | a few minutes to run. 6 | ''' 7 | 8 | from __future__ import print_function, division 9 | import sys 10 | import numpy as np 11 | from Bio import Phylo 12 | 13 | import matplotlib.pyplot as plt 14 | from matplotlib import cm 15 | try: 16 | import seaborn as sns 17 | sns.set_style('whitegrid') 18 | except: 19 | print ("Seaborn not found. Default style will be used for the plots") 20 | 21 | from treetime import TreeTime 22 | from treetime.utils import parse_dates 23 | import treetime.config as ttconf 24 | 25 | if __name__ == '__main__': 26 | 27 | 28 | plt.ion() 29 | base_name = '../data/ebola/ebola' 30 | dates = parse_dates(base_name+'.metadata.csv') 31 | # instantiate treetime 32 | ebola = TreeTime(gtr='Jukes-Cantor', tree = base_name+'.nwk', precision=1, 33 | aln = base_name+'.fasta', verbose = 2, dates = dates) 34 | 35 | # infer an ebola time tree while rerooting and resolving polytomies 36 | res = ebola.run(root='best', infer_gtr=True, relaxed_clock=False, max_iter=2, 37 | branch_length_mode='input', n_iqd=3, resolve_polytomies=True, 38 | Tc='skyline', time_marginal="assign", vary_rate=True) 39 | 40 | if res==ttconf.ERROR: 41 | sys.exit() 42 | 43 | # scatter root to tip divergence vs sampling date 44 | ebola.plot_root_to_tip(add_internal=True) 45 | plt.legend(loc=2) 46 | 47 | # rescale branch length to years and plot in axis 0 48 | from treetime.treetime import plot_vs_years 49 | fig, axs = plt.subplots(1,2, sharey=True, figsize=(12,8)) 50 | plot_vs_years(ebola, step=1, ax=axs[1], confidence=(0.05,0.95), label_func = lambda x:"") 51 | axs[1].set_xlim(0, 2.5) 52 | axs[1].set_title("time tree") 53 | 54 | # assign mutation length to branch length and plot the mutation tree in axs[1] 55 | axs[0].set_title("mutation tree") 56 | for n in ebola.tree.find_clades(): 57 | n.branch_length=n.mutation_length 58 | Phylo.draw(ebola.tree, label_func=lambda x:"", axes=axs[0]) 59 | plt.tight_layout() 60 | 61 | # reset branch length to time (in substitution rate units) 62 | for n in ebola.tree.find_clades(): 63 | n.branch_length=n.clock_length 64 | 65 | # OUTPUT the GTR model 66 | print(ebola.gtr) 67 | 68 | # plot Skyline 69 | skyline, confidence = ebola.merger_model.skyline_inferred(gen=50, confidence=2.0) 70 | skyline_empirical = ebola.merger_model.skyline_empirical(gen=50) 71 | plt.figure() 72 | plt.fill_between(skyline.x, confidence[0], confidence[1], color=(0.8, 0.8, 0.8)) 73 | plt.plot(skyline.x, skyline.y, label='maximum likelihood skyline') 74 | plt.plot(skyline_empirical.x, skyline_empirical.y, label='empirical skyline') 75 | plt.yscale('log') 76 | plt.legend() 77 | plt.ticklabel_format(axis='x',useOffset=False) 78 | 79 | 80 | 81 | 82 | 83 | -------------------------------------------------------------------------------- /scripts/relaxed_clock.py: -------------------------------------------------------------------------------- 1 | """ 2 | This script illustrates the use of the relaxed clock model in TreeTime. 3 | TreeTime currently only supports a normally distributed clock model. 4 | """ 5 | 6 | from __future__ import print_function, division 7 | import sys 8 | import numpy as np 9 | from Bio import Phylo 10 | 11 | import matplotlib.pyplot as plt 12 | from matplotlib import cm 13 | try: 14 | import seaborn as sns 15 | sns.set_style('whitegrid') 16 | except: 17 | print ("Seaborn not found. Default style will be used for the plots") 18 | 19 | from treetime import TreeTime 20 | from treetime.utils import parse_dates 21 | import treetime.config as ttconf 22 | 23 | 24 | if __name__ == '__main__': 25 | 26 | # load data and parse dates 27 | plt.ion() 28 | base_name = '../data/h3n2_na/h3n2_na_20' 29 | dates = parse_dates(base_name+'.metadata.csv') 30 | 31 | # instantiate treetime 32 | tt_relaxed = TreeTime(gtr='Jukes-Cantor', tree = base_name+'.nwk', 33 | aln = base_name+'.fasta', verbose = 4, dates = dates) 34 | 35 | # this example uses an autocorrelated molecular clock with normal prior and parent-child coupling 36 | # the parameter slack penalizes rate deviations from the average rate 37 | # couplings penalize rate changes between parent and child nodes. 38 | tt_relaxed.run(root='best', relaxed_clock={"slack":5.0, "coupling":1.0}, max_iter=3, 39 | resolve_polytomies=True, Tc=0, time_marginal=False) 40 | 41 | 42 | 43 | ############## 44 | # PLOTTING 45 | ############## 46 | 47 | # draw trees inferred with the relaxed model 48 | fig = plt.figure() 49 | ax = plt.subplot(111) 50 | vmin, vmax = 0.5, 1.5 # color branches according to the rate deviation 51 | for n in tt_relaxed.tree.find_clades(): 52 | if n.up: 53 | n.color = [int(x*255) for x in cm.cool((min(max(vmin, n.branch_length_interpolator.gamma),vmax)-vmin)/(vmax-vmin))[:3]] 54 | else: 55 | n.color = [200,200,200] 56 | 57 | ax.set_title("relaxed clock") 58 | Phylo.draw(tt_relaxed.tree, axes=ax, show_confidence=False, label_func = lambda x:'') 59 | 60 | # Scatter branch stretch against the rate multiplier of the branch. 61 | # they are expected to have a positive correlation 62 | # 1) collect the optimal branch lenght (called mutation_length), 63 | # the timetree branch length (clock_length) and the inferred rate multiplier gamma 64 | branch_lengths = [] 65 | for n in tt_relaxed.tree.find_clades(): 66 | if n.up: 67 | branch_lengths.append((n.mutation_length, n.clock_length, n.branch_length_interpolator.gamma)) 68 | 69 | 70 | # 2) plot the difference between optimal and timetree branch length vs the rate multiplier 71 | plt.figure() 72 | branch_lengths = np.array(branch_lengths) 73 | plt.scatter(branch_lengths[:,0]-branch_lengths[:,1], branch_lengths[:,2]) 74 | plt.xlabel("stretch") 75 | plt.ylabel("rate multiplier") 76 | 77 | 78 | -------------------------------------------------------------------------------- /scripts/rerooting_and_timetrees.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function, division 2 | import numpy as np 3 | from Bio import Phylo 4 | import matplotlib.pyplot as plt 5 | from matplotlib import cm 6 | try: 7 | import seaborn as sns 8 | sns.set_style('whitegrid') 9 | except: 10 | print ("Seaborn not found. Default style will be used for the plots") 11 | 12 | from treetime import TreeTime 13 | from treetime.utils import parse_dates 14 | 15 | def format_axes(fig, axs): 16 | axs[0].set_axis_off() 17 | axs[1].tick_params(labelsize=14) 18 | axs[1].set_ylabel("root-to-tip distance", fontsize=16) 19 | axs[1].set_xlabel("date", fontsize=16) 20 | fig.tight_layout() 21 | 22 | 23 | if __name__ == '__main__': 24 | 25 | # load data and parse dates 26 | plt.ion() 27 | base_name = '../data/h3n2_na/h3n2_na_20' 28 | 29 | dates = parse_dates(base_name+'.metadata.csv') 30 | tt = TreeTime(gtr='Jukes-Cantor', tree = base_name+'.nwk', 31 | aln = base_name+'.fasta', verbose = 1, dates = dates) 32 | 33 | # inititally the root if the tree is a mess: 34 | fig, axs = plt.subplots(1,2, figsize=(18,9)) 35 | axs[0].set_title("Arbitrarily rooted tree", fontsize=18) 36 | axs[1].set_title("Inverse divergence-time relationship", fontsize=18) 37 | Phylo.draw(tt.tree, show_confidence=False, axes=axs[0], label_func=lambda x:x.name.split('|')[0] if x.is_terminal() else "") 38 | tt.plot_root_to_tip(ax=axs[-1]) 39 | format_axes(fig, axs) 40 | 41 | # lets reroot: we now have a positve correlation of root-to-tip distance with sampling date 42 | tt.reroot(root="least-squares") 43 | fig, axs = plt.subplots(1,2, figsize=(18,9)) 44 | axs[0].set_title("Tree rerooted by treetime", fontsize=18) 45 | axs[1].set_title("Optimal divergence-time relationship", fontsize=18) 46 | Phylo.draw(tt.tree, show_confidence=False, axes=axs[0], 47 | label_func=lambda x:x.name.split('|')[0] if x.is_terminal() else "") 48 | tt.plot_root_to_tip(ax=axs[-1]) 49 | format_axes(fig, axs) 50 | 51 | # rerooting can be done along with the tree time inference 52 | tt.run(root="best", branch_length_mode='input', max_iter=2) 53 | # if more complicated models (relaxed clocks, coalescent models) are to be used 54 | # or you want to resolve polytomies, treetime needs to be run for 55 | # several iterations, for example as 56 | # tt.run(root="best", resolve_polytomies=True, max_iter=2) 57 | 58 | # each node is now at a position that correspond to the given or inferred date 59 | # the units of branch length are still clock rate. 60 | print("clock rate: %1.5f"%tt.date2dist.clock_rate) 61 | fig, axs = plt.subplots(1,2, figsize=(18,9)) 62 | Phylo.draw(tt.tree, label_func=lambda x:'', show_confidence=False, axes=axs[0]) 63 | axs[0].set_title("Tree: units are substitutions", fontsize=18) 64 | 65 | # we can convert the branch length to units in years and redraw 66 | tt.branch_length_to_years() 67 | Phylo.draw(tt.tree, label_func=lambda x:'', show_confidence=False, axes=axs[1]) 68 | axs[1].set_title("Tree: units are years", fontsize=18) 69 | axs[0].tick_params(labelsize=14) 70 | axs[1].tick_params(labelsize=14) 71 | fig.tight_layout() 72 | 73 | # treetime implements a convenience function to plot timetrees 74 | from treetime.treetime import plot_vs_years 75 | plot_vs_years(tt, label_func=lambda x:"", show_confidence=False) 76 | 77 | --------------------------------------------------------------------------------