├── figures ├── corr.png ├── map.png ├── drift.png ├── jumps.png ├── trees.png ├── seq_grid.png ├── counts_corr.png ├── hij_likelihood.png ├── schematic_map.png ├── smith_comparison.png ├── smith_comparison_drift.png ├── smith_comparison_effects.png ├── error_by_distance_and_year.png └── smith_comparison_rotation.png ├── figure-data ├── README.md ├── fig05_year_to_year_drift.tsv ├── fig09_smith_mds.tsv ├── fig10_smith_mds_rotation.tsv ├── fig11_smith_mds_drift.tsv └── fig12_smith_mds_effects.tsv ├── data ├── incidence_data.tsv ├── H1N1_seq_data.tsv ├── Yam_seq_data.tsv ├── Vic_seq_data.tsv └── H3N2_seq_data.tsv ├── .gitignore ├── example-xmls ├── H1N1_mds_nodrift_noeffects_notree.xml ├── H1N1_mds_drift_noeffects_notree.xml ├── H1N1_mds_drift_effects_notree.xml ├── README.md └── H1N1_mds_drift_effects_tree.xml ├── README.md ├── correspondence ├── cover_letter.tex └── reresponse.tex └── Rakefile /figures/corr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/corr.png -------------------------------------------------------------------------------- /figures/map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/map.png -------------------------------------------------------------------------------- /figures/drift.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/drift.png -------------------------------------------------------------------------------- /figures/jumps.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/jumps.png -------------------------------------------------------------------------------- /figures/trees.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/trees.png -------------------------------------------------------------------------------- /figures/seq_grid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/seq_grid.png -------------------------------------------------------------------------------- /figures/counts_corr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/counts_corr.png -------------------------------------------------------------------------------- /figures/hij_likelihood.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/hij_likelihood.png -------------------------------------------------------------------------------- /figures/schematic_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/schematic_map.png -------------------------------------------------------------------------------- /figures/smith_comparison.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/smith_comparison.png -------------------------------------------------------------------------------- /figures/smith_comparison_drift.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/smith_comparison_drift.png -------------------------------------------------------------------------------- /figures/smith_comparison_effects.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/smith_comparison_effects.png -------------------------------------------------------------------------------- /figures/error_by_distance_and_year.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/error_by_distance_and_year.png -------------------------------------------------------------------------------- /figures/smith_comparison_rotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trvrb/flux/HEAD/figures/smith_comparison_rotation.png -------------------------------------------------------------------------------- /figure-data/README.md: -------------------------------------------------------------------------------- 1 | ## Figure data 2 | 3 | These represent `.tsv` files that give virus and serum locations for Figures 2, 3, 9, 10, 11 and 12 in the manuscript. Additionally, data for antigenic jumps in Figure 5 are provided. 4 | -------------------------------------------------------------------------------- /data/incidence_data.tsv: -------------------------------------------------------------------------------- 1 | startYear endYear flu typeA typeB subtypeH3 subtypeH1 subtypeH1pdm subtypeVic subtypeYam ili 2 | 1998 1999 14 72 28 99 1 0 0 100 2.10 3 | 1999 2000 15 99 1 97 3 0 0 100 1.83 4 | 2000 2001 11 54 46 3 97 0 0 100 2.05 5 | 2001 2002 16 87 13 98 2 0 77 23 1.70 6 | 2002 2003 11 56 44 30 70 0 100 0 1.47 7 | 2003 2004 19 99 1 100 0 0 7 93 1.98 8 | 2004 2005 15 75 25 99 1 0 26 74 1.88 9 | 2005 2006 12 80 20 92 8 0 81 19 1.65 10 | 2006 2007 13 79 21 38 62 0 77 23 1.63 11 | 2007 2008 18 71 29 74 26 0 2 98 1.97 12 | 2008 2009 14 66 34 13 87 0 83 17 1.95 13 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # For flux repo # 2 | flux.pdf 3 | flux_si.pdf 4 | cover_letter.pdf 5 | response.pdf 6 | reresponse.pdf 7 | 8 | # Compiled source # 9 | ################### 10 | *.com 11 | *.class 12 | *.dll 13 | *.exe 14 | *.o 15 | *.so 16 | 17 | # LaTeX intermediaries # 18 | ######################## 19 | *.aux 20 | *.log 21 | *.bbl 22 | *.blg 23 | *.out 24 | 25 | # Packages # 26 | ############ 27 | *.7z 28 | *.dmg 29 | *.gz 30 | *.iso 31 | *.jar 32 | *.rar 33 | *.tar 34 | *.zip 35 | 36 | # OS generated files # 37 | ###################### 38 | .DS_Store 39 | .DS_Store? 40 | ._* 41 | .Spotlight-V100 42 | .Trashes 43 | Icon? 44 | ehthumbs.db 45 | Thumbs.db -------------------------------------------------------------------------------- /example-xmls/H1N1_mds_nodrift_noeffects_notree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Integrating influenza antigenic dynamics with molecular evolution 2 | 3 | Trevor Bedford1, Marc A. Suchard2,3,4, Philippe Lemey5, Gytis 4 | Dudas1, Victoria Gregory6, Alan J. Hay6, John W. 5 | McCauley6, Colin A. Russell7,8, Derek J. Smith7,8,9, Andrew 6 | Rambaut1,10 7 | 8 | 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK, 9 | 2Department of Biomathematics, David Geffen School of Medicine at UCLA, University of 10 | California, Los Angeles CA, USA, 3Department of Human Genetics, David Geffen School of 11 | Medicine at UCLA, University of California, Los Angeles CA, USA, 4Department of 12 | Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles CA, USA, 13 | 5Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, 14 | Belgium, 6Division of Virology, MRC National Institute for Medical Research, Mill Hill, 15 | London, UK, 7Centre for Pathogen Evolution, Department of Zoology, University of 16 | Cambridge, Cambridge, UK, 8WHO Collaborating Center for Modeling, Evolution, and Control 17 | of Emerging Infectious Diseases, University of Cambridge, Cambridge, UK, 9Department of 18 | Virology, Erasmus Medical Centre, Rotterdam, Netherlands, 10Fogarty International Center, 19 | National Institutes of Health, Bethesda, MD, USA 20 | 21 | ## Citation 22 | 23 | [Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, 24 | Rambaut A. 2014. Integrating influenza antigenic dynamics with molecular evolution. eLife 3: e01914.](http://dx.doi.org/10.7554/elife.01914) 25 | 26 | ## Abstract 27 | 28 | Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host 29 | immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise 30 | measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) 31 | assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize 32 | antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus 33 | phylogeny. Using HI data from influenza A subtypes H3N2 and H1N1 and influenza B lineages Victoria 34 | and Yamagata, we determine patterns of antigenic drift across lineages and show that antigenic drift 35 | drives incidence rates and mediates interference between influenza lineages. Additionally, we 36 | describe the selective underpinnings of differences in antigenic drift across lineages. This work 37 | makes possible substantial future advances in investigating the dynamics of influenza and other 38 | antigenically-variable pathogens by providing a model that intimately combines molecular and 39 | antigenic evolution. 40 | 41 | ## Instructions 42 | 43 | Run `rake`. If LaTeX is installed, this will compile all the `.tex` documents in the repo. 44 | 45 | ## License 46 | 47 | This work is licensed under a [Creative Commons Attribution 3.0 Unported License](http://creativecommons.org/licenses/by/3.0/deed.en_US). -------------------------------------------------------------------------------- /correspondence/cover_letter.tex: -------------------------------------------------------------------------------- 1 | \documentclass[stdletter,letterpaper,addrfromright,orderfromdateto,dateleft,11pt,noaddrto,sigleft]{newlfm} 2 | \topmarginskip{-0.4in} 3 | \bottommarginskip{-1.5in} 4 | \leftmarginsize{1in} 5 | \rightmarginsize{1.25in} 6 | \sigskipbefore{0.2in} 7 | \sigskipafter{0in} 8 | \noLines 9 | \nolines 10 | \noHeadline 11 | \noheadline 12 | \signature{Trevor Bedford} 13 | 14 | \namefrom{} 15 | \addrfrom{Inst.\ of Evolutionary Biology \\ University of Edinburgh \\ Ashworth Laboratories \\ King's Buildings \\ Edinburgh, UK} 16 | \phonefrom{(617) 285-2542} 17 | \faxfrom{(734) 763-0544} 18 | \emailfrom{bedfordt@umich.edu} 19 | 20 | \greetto{Dear Editor,} 21 | \closeline{Sincerely,} 22 | 23 | % comments 24 | \usepackage{color} 25 | \usepackage{ulem} 26 | \definecolor{purple}{rgb}{0.459,0.109,0.538} 27 | \def\tb#1#2{\sout{#1} \textcolor{purple}{#2}} 28 | \def\tbc#1{\textcolor{purple}{[#1]}} 29 | 30 | \begin{document} 31 | 32 | \begin{newlfm} 33 | 34 | Please find, attached, our manuscript entitled ``Integrating influenza antigenic dynamics with molecular evolution,'' which we would be grateful for your consideration for publication in \textit{eLife}. 35 | We believe that \textit{eLife} is an appropriate venue for this work, as it clarifies long-standing questions about the antigenic and evolutionary dynamics of influenza viruses, while simultaneously presenting a major methodological advance in the characterization of antigenic phenotype. 36 | 37 | Since the publication of ``Mapping the Antigenic and Genetic Evolution of Influenza Virus'' by Smith et al.\ in 2004, there has been significant interest in assessing patterns of antigenic and genetic evolution in seasonal influenza. 38 | Such cartographic approaches use multidimensional scaling (MDS) to position viruses and antisera on an antigenic map so that distances between viruses and antisera predict observed serological data. 39 | Here, we present a substantial advance to previous approaches that uses Bayesian multidimensional scaling (BMDS) to place antigenic cartography in a fully probabilistic framework. 40 | Doing so has allowed us to build in important covariates into the statistical model; most importantly, phylogenetic relationships. 41 | Thus, our method simultaneously models evolutionary and antigenic dynamics, and allows us to infer which phylogeny branches have evolved in antigenic phenotype and which branches have remained static. 42 | 43 | We test our method with substantial new datasets for influenza A/H3N2, A/H1N1, B/Victoria and B/Yamagata, presenting, for the first time, detailed evolutionary and antigenic reconstructions for all four major circulating lineages. 44 | We find that influenza A/H3N2 shows the fastest and most punctuated evolution of antigenic phenotype relative to the other three circulating lineages. 45 | We connect antigenic evolution to incidence patterns, showing that antigenic drift leading into an influenza season accounts for 46\% of the variance in seasonal incidence. 46 | This analysis shows a strong signal of interference between lineages, with antigenic drift in a sister lineage having a negative impact on within-lineage incidence. 47 | Additionally, we've used phylogenetic information to characterize fundamental differences in antigenic dynamics between lineages, finding that A/H3N2 benefits from both a greater influx of new antigenic mutations and from a more rapid spread of these mutations through the population. 48 | 49 | Both the link between incidence and antigenic drift and the presence of interference across influenza subtypes have remained long-standing questions in the influenza community. 50 | We believe our results do much to address these questions. 51 | Additionally, we believe our methodological advances will prove fundamental to future research in influenza and other antigenically variable pathogens. 52 | Our unified genetic / antigenic approach will make it possible to look closely for causal relationships between genetic mutations and antigenic change, and to characterize, for the first time, the antigenic mutations that are ultimately successful in the global competition among virus lineages. 53 | 54 | \end{newlfm} 55 | \end{document} -------------------------------------------------------------------------------- /Rakefile: -------------------------------------------------------------------------------- 1 | # Rakefile to collect all .tex files in a directory and run `pdflatex` and `bibtex` as needed to 2 | # produce PDF output. If a .tex file is updated `pdflatex -draftmode` will be run to produce new 3 | # .aux and .log files. These are used to determine whether `bibtex` needs to be run. If so `bibtex` 4 | # will always need to be followed by `pdflatex -draftmode`. With fully updated .aux and .bbl in 5 | # hand, a final `pdflatex` is run. The only hole in the logic I've found is that, when making a 6 | # small revision, this will run `pdflatex -draftmode` then `pdflatex` when only `pdflatex` is 7 | # required. 8 | # 9 | # Run `rake` to compile PDFs and `rake clean` to remove the intermediary cruft 10 | 11 | basedir = Dir.getwd 12 | 13 | TEX = FileList["**/*.tex"] 14 | AUX = TEX.ext("aux") 15 | BBL = TEX.ext("bbl") 16 | BLG = TEX.ext("blg") 17 | LOG = TEX.ext("log") 18 | OUT = TEX.ext("out") 19 | PDF = TEX.ext("pdf") 20 | 21 | require 'rake/clean' 22 | CLEAN.include(AUX) 23 | CLEAN.include(BBL) 24 | CLEAN.include(BLG) 25 | CLEAN.include(LOG) 26 | CLEAN.include(OUT) 27 | CLOBBER.include(PDF) 28 | 29 | desc "Full compile" 30 | task :default => PDF 31 | 32 | desc "LaTeX aux" 33 | rule ".aux" => ".tex" do |t| 34 | prefix = t.name.pathmap("%n") 35 | dir = t.name.pathmap("%d") 36 | Dir.chdir(dir) 37 | puts "pdflatex -draftmode #{prefix}" 38 | `pdflatex -draftmode #{prefix}` 39 | Dir.chdir(basedir) 40 | end 41 | 42 | desc "LaTeX log" 43 | rule ".log" => ".tex" do |t| 44 | prefix = t.name.pathmap("%n") 45 | dir = t.name.pathmap("%d") 46 | Dir.chdir(dir) 47 | puts "pdflatex -draftmode #{prefix}" 48 | `pdflatex -draftmode #{prefix}` 49 | Dir.chdir(basedir) 50 | end 51 | 52 | desc "LaTeX compile" 53 | # require log file and proceed if references are incomplete 54 | rule ".pdf" => [".aux", ".bbl", ".log", ".tex"] do |t| 55 | prefix = t.name.pathmap("%n") 56 | dir = t.name.pathmap("%d") 57 | Dir.chdir(dir) 58 | puts "pdflatex #{prefix}" 59 | `pdflatex #{prefix}` 60 | Dir.chdir(basedir) 61 | end 62 | 63 | desc "BibTex compile" 64 | # look for .bib file in top-level directory 65 | rule ".bbl" => [".aux", ".log", ".tex"] do |t| 66 | prefix = t.name.pathmap("%n") 67 | dir = t.name.pathmap("%d") 68 | Dir.chdir(dir) 69 | if cite?(prefix) 70 | puts "bibtex #{prefix}" 71 | `bibtex #{prefix}` 72 | puts "pdflatex -draftmode #{prefix}" 73 | `pdflatex -draftmode #{prefix}` 74 | end 75 | Dir.chdir(basedir) 76 | end 77 | 78 | desc "Look at log file and check if references are complete" 79 | def ref?(string) 80 | dirty = false 81 | file = File.open("#{string}.log", "r") 82 | m = file.read.match(/LaTeX Warning: There were undefined references|LaTeX Warning: Label(s) may have changed. Rerun to get|^LaTeX Warning: Reference/) 83 | file.close 84 | if m != nil 85 | puts m 86 | dirty = true 87 | end 88 | return dirty 89 | end 90 | 91 | desc "Are citations up to date?" 92 | def cite?(string) 93 | dirty = false 94 | if File.exists?("#{string}.bbl") 95 | if cite_missing(string) == true 96 | dirty = true 97 | else 98 | aux_list = cite_aux(string) 99 | bbl_list = cite_bbl(string) 100 | extra = (aux_list - bbl_list).length 101 | missing = (bbl_list - aux_list).length 102 | if extra > 0 || missing > 0 103 | dirty = true 104 | end 105 | end 106 | else 107 | dirty = true 108 | end 109 | return dirty 110 | end 111 | 112 | desc "Look at log file and check if citations are complete" 113 | def cite_missing(string) 114 | dirty = false 115 | file = File.open("#{string}.log", "r") 116 | m = file.read.match(/^LaTeX Warning: Citation/) 117 | file.close 118 | if m != nil 119 | puts m 120 | dirty = true 121 | end 122 | return dirty 123 | end 124 | 125 | desc "Find citations in .aux" 126 | def cite_aux(string) 127 | list = Array.new 128 | file = File.open("#{string}.aux", "r") 129 | cites = file.read.scan(/\\citation{([^\}]+)}/) 130 | file.close 131 | if cites != nil 132 | cites.each {|m| 133 | list += m[0].split(",") 134 | } 135 | end 136 | list.uniq! 137 | return list 138 | end 139 | 140 | desc "Find citations in .bbl" 141 | def cite_bbl(string) 142 | list = Array.new 143 | file = File.open("#{string}.bbl", "r") 144 | cites = file.read.scan(/\\bibitem{([^\}]+)}/) 145 | file.close 146 | if cites != nil 147 | cites.each {|m| 148 | list += m[0].split(",") 149 | } 150 | end 151 | list.uniq! 152 | return list 153 | end -------------------------------------------------------------------------------- /figure-data/fig05_year_to_year_drift.tsv: -------------------------------------------------------------------------------- 1 | statistic virus time lower mean upper 2 | xdrift H3N2 1968 1.22205 1.55264 1.87057 3 | xdrift H3N2 1969 0.0714186 0.25858 0.446792 4 | xdrift H3N2 1970 -0.0509345 0.133018 0.310638 5 | xdrift H3N2 1971 0.654708 0.850586 1.03494 6 | xdrift H3N2 1972 1.81264 2.03252 2.24436 7 | xdrift H3N2 1973 0.719834 0.880729 1.03754 8 | xdrift H3N2 1974 0.555152 0.707491 0.868667 9 | xdrift H3N2 1975 0.900497 1.07832 1.25031 10 | xdrift H3N2 1976 2.41887 2.61127 2.80678 11 | xdrift H3N2 1977 0.0577463 0.173096 0.297578 12 | xdrift H3N2 1978 1.74782 2.09045 2.4664 13 | xdrift H3N2 1979 0.653349 0.919863 1.17894 14 | xdrift H3N2 1980 -0.204996 0.0160854 0.248883 15 | xdrift H3N2 1981 0.41944 0.622973 0.828516 16 | xdrift H3N2 1982 0.0405576 0.224755 0.416174 17 | xdrift H3N2 1983 -0.0148089 0.261564 0.521369 18 | xdrift H3N2 1984 0.329347 0.581147 0.844088 19 | xdrift H3N2 1985 0.297857 0.554339 0.792721 20 | xdrift H3N2 1986 0.490205 0.678741 0.861682 21 | xdrift H3N2 1987 1.58365 1.75901 1.93881 22 | xdrift H3N2 1988 0.772448 0.898188 1.03575 23 | xdrift H3N2 1989 1.1751 1.29469 1.40533 24 | xdrift H3N2 1990 0.262294 0.404305 0.554112 25 | xdrift H3N2 1991 0.218734 0.360643 0.509901 26 | xdrift H3N2 1992 1.57552 1.68803 1.80542 27 | xdrift H3N2 1993 3.35341 3.48203 3.60951 28 | xdrift H3N2 1994 0.847397 0.945131 1.05681 29 | xdrift H3N2 1995 0.432631 0.538292 0.647198 30 | xdrift H3N2 1996 -0.0765554 0.0679823 0.201182 31 | xdrift H3N2 1997 1.62807 1.79019 1.95046 32 | xdrift H3N2 1998 1.31689 1.49279 1.68141 33 | xdrift H3N2 1999 0.59502 0.792045 0.982596 34 | xdrift H3N2 2000 0.108639 0.254778 0.404688 35 | xdrift H3N2 2001 0.449798 0.626663 0.80584 36 | xdrift H3N2 2002 0.975448 1.17204 1.3739 37 | xdrift H3N2 2003 1.16183 1.25758 1.34667 38 | xdrift H3N2 2004 1.64748 1.74003 1.8345 39 | xdrift H3N2 2005 1.02213 1.10908 1.19328 40 | xdrift H3N2 2006 0.364918 0.481224 0.590556 41 | xdrift H3N2 2007 1.1344 1.28472 1.44559 42 | xdrift H3N2 2008 0.272693 0.469952 0.645912 43 | xdrift H3N2 2009 3.69326 3.84705 4.01218 44 | xdrift H3N2 2010 0.366977 0.518883 0.675054 45 | xdrift H3N2 2011 0.609007 0.79425 0.976931 46 | xdrift H1N1 1977 0.255587 0.569117 0.881899 47 | xdrift H1N1 1978 0.889382 1.11854 1.34788 48 | xdrift H1N1 1979 0.213492 0.622344 1.04858 49 | xdrift H1N1 1980 0.492565 0.773609 1.04378 50 | xdrift H1N1 1981 0.450111 0.562868 0.679928 51 | xdrift H1N1 1982 0.418339 0.512583 0.615397 52 | xdrift H1N1 1983 0.418339 0.512583 0.615397 53 | xdrift H1N1 1984 1.92898 2.18717 2.43701 54 | xdrift H1N1 1985 0.767811 0.874061 0.989823 55 | xdrift H1N1 1986 0.439089 0.718026 0.993694 56 | xdrift H1N1 1987 -0.381316 -0.159536 0.0661004 57 | xdrift H1N1 1988 0.0120726 0.192166 0.36343 58 | xdrift H1N1 1989 0.0654428 0.294876 0.526215 59 | xdrift H1N1 1990 -0.123043 0.251287 0.602668 60 | xdrift H1N1 1991 0.238535 0.471125 0.701801 61 | xdrift H1N1 1992 0.374216 0.593335 0.821332 62 | xdrift H1N1 1993 0.0399577 0.357692 0.657011 63 | xdrift H1N1 1994 0.150487 0.466465 0.819923 64 | xdrift H1N1 1995 0.378559 0.576443 0.765315 65 | xdrift H1N1 1996 0.196943 0.651304 1.10133 66 | xdrift H1N1 1997 2.239 2.68067 3.10022 67 | xdrift H1N1 1998 0.230692 0.498687 0.766439 68 | xdrift H1N1 1999 0.352872 0.616994 0.875605 69 | xdrift H1N1 2000 -0.363181 -0.113898 0.151258 70 | xdrift H1N1 2001 -0.598507 -0.33044 -0.0700414 71 | xdrift H1N1 2002 0.116719 0.329078 0.537317 72 | xdrift H1N1 2003 0.252553 0.403065 0.549741 73 | xdrift H1N1 2004 0.0413044 0.251156 0.460427 74 | xdrift H1N1 2005 0.318995 0.471619 0.620401 75 | xdrift H1N1 2006 1.45708 1.62833 1.80035 76 | xdrift H1N1 2007 0.92765 1.07881 1.21976 77 | xdrift H1N1 2008 0.511941 0.66795 0.817877 78 | xdrift H1N1 2009 0.324602 0.508705 0.707787 79 | xdrift Vic 1986 0.336059 0.549775 0.764229 80 | xdrift Vic 1987 0.178997 0.5109 0.826743 81 | xdrift Vic 1988 -0.828184 -0.457787 -0.0839455 82 | xdrift Vic 1989 -0.0832276 0.777665 1.61004 83 | xdrift Vic 1990 -0.18493 0.074906 0.322893 84 | xdrift Vic 1991 -0.110453 0.159308 0.427114 85 | xdrift Vic 1992 0.00870881 0.235518 0.461718 86 | xdrift Vic 1993 0.0224373 0.259811 0.496651 87 | xdrift Vic 1994 0.40825 0.64119 0.863525 88 | xdrift Vic 1995 0.236168 0.588348 0.920715 89 | xdrift Vic 1996 0.37096 0.673161 0.949987 90 | xdrift Vic 1997 0.311013 0.604363 0.891426 91 | xdrift Vic 1998 -0.54271 -0.249222 0.0357265 92 | xdrift Vic 1999 -0.230271 0.0295594 0.3 93 | xdrift Vic 2000 -0.225298 0.078864 0.395163 94 | xdrift Vic 2001 0.0807208 0.284473 0.515021 95 | xdrift Vic 2002 0.082918 0.279552 0.470849 96 | xdrift Vic 2003 0.0941555 0.342833 0.601466 97 | xdrift Vic 2004 0.145058 0.360106 0.581818 98 | xdrift Vic 2005 -0.247816 -0.000301654 0.226891 99 | xdrift Vic 2006 0.368842 0.552316 0.735281 100 | xdrift Vic 2007 0.201414 0.385098 0.574546 101 | xdrift Vic 2008 1.14123 1.36883 1.59261 102 | xdrift Vic 2009 0.822478 1.02498 1.22765 103 | xdrift Vic 2010 1.24853 1.40368 1.56159 104 | xdrift Vic 2011 -0.504232 -0.352658 -0.208851 105 | xdrift Yam 1987 0.133144 0.294212 0.453782 106 | xdrift Yam 1988 0.0650784 0.240599 0.414957 107 | xdrift Yam 1989 -0.582081 -0.285453 0.0166306 108 | xdrift Yam 1990 0.280678 0.447984 0.616798 109 | xdrift Yam 1991 0.669197 0.901822 1.13252 110 | xdrift Yam 1992 0.209909 0.411921 0.604771 111 | xdrift Yam 1993 0.271468 0.410553 0.539735 112 | xdrift Yam 1994 0.450173 0.612413 0.773473 113 | xdrift Yam 1995 -0.451739 -0.109329 0.219112 114 | xdrift Yam 1996 0.0632975 0.272869 0.488553 115 | xdrift Yam 1997 0.120272 0.312052 0.498651 116 | xdrift Yam 1998 0.188884 0.339204 0.485223 117 | xdrift Yam 1999 0.0298671 0.171629 0.30828 118 | xdrift Yam 2000 0.122209 0.304214 0.467003 119 | xdrift Yam 2001 0.06456 0.249772 0.432518 120 | xdrift Yam 2002 -0.186857 0.0142857 0.207303 121 | xdrift Yam 2003 -0.370907 -0.115676 0.151582 122 | xdrift Yam 2004 0.225086 0.399547 0.575007 123 | xdrift Yam 2005 0.204485 0.36761 0.528363 124 | xdrift Yam 2006 0.443844 0.685634 0.927738 125 | xdrift Yam 2007 0.24354 0.408921 0.568656 126 | xdrift Yam 2008 0.613693 0.784376 0.959596 127 | xdrift Yam 2009 0.705651 0.849278 0.98235 128 | xdrift Yam 2010 0.0356721 0.161 0.281054 129 | xdrift Yam 2011 0.203322 0.353096 0.505647 130 | -------------------------------------------------------------------------------- /data/H1N1_seq_data.tsv: -------------------------------------------------------------------------------- 1 | strain accession type subtype year database 2 | A/Annecy/2013/2009 EPI_ISL_68855 A H1N1 2009 GISAID 3 | A/Arizona/14/1978 EPI_ISL_6855 A H1N1 1978 GISAID 4 | A/Bangkok/1544/2004 EPI_ISL_21808 A H1N1 2004 GISAID 5 | A/Bayern/7/1995 EPI_ISL_2663 A H1N1 1995 GISAID 6 | A/Beijing/262/1995 EPI_ISL_2656 A H1N1 1995 GISAID 7 | A/Berlin/59/2008 EPI_ISL_65494 A H1N1 2008 GISAID 8 | A/Brazil/11/1978 CY020293 A H1N1 1978 IRD 9 | A/Brisbane/59/2007 CY030232 A H1N1 2007 IRD 10 | A/California/45/1978 EPI_ISL_8078 A H1N1 1978 GISAID 11 | A/Chile/1/1983 CY121261 A H1N1 1983 IRD 12 | A/Dakar/88/2003 EPI_ISL_100343 A H1N1 2003 GISAID 13 | A/Denmark/22/2005 EPI_ISL_15603 A H1N1 2005 GISAID 14 | A/Denmark/3/2005 EPI_ISL_15929 A H1N1 2005 GISAID 15 | A/Denmark/56/2003 EU097960 A H1N2 2003 IRD 16 | A/Denmark/86/2003 EU097959 A H1N2 2003 IRD 17 | A/Egypt/10/2007 EPI_ISL_106505 A H1N1 2007 GISAID 18 | A/Egypt/136/2005 EPI_ISL_100332 A H1N1 2005 GISAID 19 | A/Egypt/96/2002 EPI_ISL_100349 A H1N1 2002 GISAID 20 | A/England/2/2002 AJ457911 A H1N2 2002 IRD 21 | A/England/333/1980 X00031 A H1N1 1980 IRD 22 | A/Finland/4/2007 EPI_ISL_18611 A H1N1 2007 GISAID 23 | A/Florida/4/2004 EPI_ISL_6292 A H1N1 2004 GISAID 24 | A/Fukushima/141/2006 EPI_ISL_20402 A H1N1 2006 GISAID 25 | A/Ghana/152/2008 EPI_ISL_65438 A H1N1 2008 GISAID 26 | A/Ghana/163/2008 EPI_ISL_65439 A H1N1 2008 GISAID 27 | A/Ghana/2/2008 EPI_ISL_65444 A H1N1 2008 GISAID 28 | A/Ghana/9/2008 EPI_ISL_65445 A H1N1 2008 GISAID 29 | A/Ghana/FS-09-718/2009 EPI_ISL_60087 A H1N1 2009 GISAID 30 | A/Ghana/FS-09-791/2009 EPI_ISL_60086 A H1N1 2009 GISAID 31 | A/Gyeonggibuk/4500/2008 EPI_ISL_65491 A H1N1 2008 GISAID 32 | A/HongKong/1252/2000 EPI_ISL_100361 A H1N1 2000 GISAID 33 | A/HongKong/18106/2009 EPI_ISL_65516 A H1N1 2009 GISAID 34 | A/HongKong/1856/2008 EPI_ISL_60838 A H1N1 2008 GISAID 35 | A/HongKong/1870/2008 CY121648 A H1N1 2008 IRD 36 | A/HongKong/1988/2009 EPI_ISL_60080 A H1N1 2009 GISAID 37 | A/HongKong/2387/2007 EPI_ISL_20749 A H1N1 2007 GISAID 38 | A/HongKong/2613/2007 EPI_ISL_20750 A H1N1 2007 GISAID 39 | A/HongKong/2652/2006 EPI_ISL_18806 A H1N1 2006 GISAID 40 | A/HongKong/3176/2008 EPI_ISL_65481 A H1N1 2008 GISAID 41 | A/HongKong/33597/2009 EPI_ISL_68854 A H1N1 2009 GISAID 42 | A/HongKong/34079/2009 EPI_ISL_68856 A H1N1 2009 GISAID 43 | A/HongKong/35/2006 EPI_ISL_22021 A H1N1 2006 GISAID 44 | A/HongKong/4580/2004 EPI_ISL_22027 A H1N1 2004 GISAID 45 | A/HongKong/4596/2004 EPI_ISL_22030 A H1N1 2004 GISAID 46 | A/HongKong/4922/2005 EPI_ISL_22040 A H1N1 2005 GISAID 47 | A/HongKong/948/2006 EPI_ISL_13560 A H1N1 2006 GISAID 48 | A/Hungary/2/2003 EPI_ISL_100339 A H1N1 2003 GISAID 49 | A/Iceland/123/2003 EPI_ISL_100344 A H1N1 2003 GISAID 50 | A/Iceland/8064/2009 EPI_ISL_65512 A H1N1 2009 GISAID 51 | A/Iceland/8599/2009 EPI_ISL_65514 A H1N1 2009 GISAID 52 | A/Incheon/2647/2007 EPI_ISL_20502 A H1N1 2007 GISAID 53 | A/Incheon/4532/2008 EPI_ISL_65492 A H1N1 2008 GISAID 54 | A/India/6263/1980 EPI_ISL_6902 A H1N1 1980 GISAID 55 | A/Johannesburg/141/2007 EPI_ISL_20671 A H1N1 2007 GISAID 56 | A/Johannesburg/28/2005 EPI_ISL_11476 A H1N1 2005 GISAID 57 | A/Johannesburg/452/2005 EPI_ISL_100328 A H1N1 2005 GISAID 58 | A/Johannesburg/5/2002 EPI_ISL_100347 A H1N1 2002 GISAID 59 | A/Johannesburg/67/2007 EPI_ISL_18817 A H1N1 2007 GISAID 60 | A/Johannesburg/82/1996 AJ457906 A H1N1 1996 IRD 61 | A/Lackland/3/1978 EPI_ISL_6869 A H1N1 1978 GISAID 62 | A/Lackland/7/1978 EPI_ISL_6870 A H1N1 1978 GISAID 63 | A/Latvia/686/2002 AJ457861 A H1N2 2002 IRD 64 | A/Madagascar/2121/2007 EPI_ISL_18660 A H1N1 2007 GISAID 65 | A/Madagascar/57794/2000 AJ457893 A H1N1 2000 IRD 66 | A/Madagascar/6054/2009 EPI_ISL_68858 A H1N1 2009 GISAID 67 | A/Madagascar/6081/2009 EPI_ISL_68859 A H1N1 2009 GISAID 68 | A/Marrakech/510/2009 EPI_ISL_65490 A H1N1 2008 GISAID 69 | A/Marseille/1148/2009 EPI_ISL_60089 A H1N1 2009 GISAID 70 | A/Mauritius/403/2008 EPI_ISL_65437 A H1N1 2008 GISAID 71 | A/Mauritius/543/2007 EPI_ISL_100326 A H1N1 2007 GISAID 72 | A/Menya/1386/2009 EPI_ISL_60090 A H1N1 2009 GISAID 73 | A/Minsk/179/2008 EPI_ISL_65425 A H1N1 2008 GISAID 74 | A/Montpellier/2051/2009 EPI_ISL_68857 A H1N1 2009 GISAID 75 | A/Morocco/275/2004 EPI_ISL_100338 A H1N1 2003 GISAID 76 | A/Moscow/2/2009 EPI_ISL_60083 A H1N1 2009 GISAID 77 | A/Netherlands/128/2004 EPI_ISL_100335 A H1N1 2004 GISAID 78 | A/Netherlands/345/2007 EPI_ISL_60837 A H1N1 2007 GISAID 79 | A/NewCaledonia/20/1999 CY031336 A H1N1 1999 IRD 80 | A/Paraguay/61/2009 EPI_ISL_34734 A H1N1 2009 GISAID 81 | A/Paris/577/2007 EPI_ISL_22843 A H1N1 2007 GISAID 82 | A/Paris/781/2008 EPI_ISL_65485 A H1N1 2008 GISAID 83 | A/Pennsylvania/1/2007 EPI_ISL_13657 A H1N1 2007 GISAID 84 | A/Perth/200/2008 EPI_ISL_22973 A H1N1 2008 GISAID 85 | A/Peru/1169/2007 EPI_ISL_20489 A H1N1 2007 GISAID 86 | A/Peru/1621/1999 EPI_ISL_1753 A H1N1 1999 GISAID 87 | A/Peru/1798/1999 EPI_ISL_1752 A H1N1 1999 GISAID 88 | A/Poitiers/2168/2003 EPI_ISL_11948 A H1N1 2003 GISAID 89 | A/Rabat/109/2009 EPI_ISL_65489 A H1N1 2008 GISAID 90 | A/Reunion/1409/2003 EPI_ISL_100337 A H1N1 2003 GISAID 91 | A/RheinlandPfalz/34/2003 FJ231790 A H1N2 2003 IRD 92 | A/Seychelles/2239/2008 EPI_ISL_60835 A H1N1 2008 GISAID 93 | A/Shenzhen/227/1995 EPI_ISL_3464 A H1N1 1995 GISAID 94 | A/Siena/10/1989 EPI_ISL_27596 A H1N1 1989 GISAID 95 | A/Siena/9/1989 EPI_ISL_27634 A H1N1 1989 GISAID 96 | A/Singapore/10/2009 EPI_ISL_60091 A H1N1 2009 GISAID 97 | A/Singapore/6/1986 EPI_ISL_6905 A H1N1 1986 GISAID 98 | A/SolomonIslands/3/2006 EU124177 A H1N1 2006 IRD 99 | A/SouthDakota/6/2007 EPI_ISL_15444 A H1N1 2007 GISAID 100 | A/Stockholm/13/2002 AJ457909 A H1N2 2002 IRD 101 | A/StPetersburg/10/2007 EPI_ISL_28439 A H1N1 2007 GISAID 102 | A/StPetersburg/12/2008 EPI_ISL_25796 A H1N1 2008 GISAID 103 | A/StPetersburg/49/2003 EPI_ISL_22333 A H1N1 2003 GISAID 104 | A/StPetersburg/5/2008 EPI_ISL_23882 A H1N1 2008 GISAID 105 | A/Switzerland/3100/2002 AJ517813 A H1N2 2002 IRD 106 | A/Taiwan/1/1986 EPI_ISL_10251 A H1N1 1986 GISAID 107 | A/Texas/36/1991 AY289927 A H1N1 1991 IRD 108 | A/Texas/5/2007 EPI_ISL_13693 A H1N1 2007 GISAID 109 | A/Thessaloniki/24/2005 EPI_ISL_100334 A H1N1 2005 GISAID 110 | A/Tula/5/2007 EPI_ISL_20434 A H1N1 2007 GISAID 111 | A/Ulaanbaatar/116/2007 EPI_ISL_20326 A H1N1 2007 GISAID 112 | A/Ulaanbaatar/2212/2007 EPI_ISL_20424 A H1N1 2007 GISAID 113 | A/USSR/90/1977 EPI_ISL_66105 A H1N1 1977 GISAID 114 | A/USSR/92/1977 EPI_ISL_5134 A H1N1 1977 GISAID 115 | A/Wisconsin/13/2009 EPI_ISL_34744 A H1N1 2009 GISAID 116 | A/Zagreb/1982/2008 FJ654325 A H1N1 2008 IRD 117 | -------------------------------------------------------------------------------- /example-xmls/H1N1_mds_drift_noeffects_notree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | -------------------------------------------------------------------------------- /data/Yam_seq_data.tsv: -------------------------------------------------------------------------------- 1 | strain accession type subtype year database 2 | B/Aichi/1/1991 EPI_ISL_27 B Yam 1991 GISAID 3 | B/Algeria/G486/2010 EPI_ISL_79601 B Yam 2010 GISAID 4 | B/Arizona/135/2005 EPI_ISL_10013 B Yam 2005 GISAID 5 | B/Bangkok/163/1990 EPI_ISL_6819 B Vic 1990 GISAID 6 | B/Bangladesh/3333/2007 EPI_ISL_20696 B Yam 2007 GISAID 7 | B/Barcelona/143/2008 EPI_ISL_100274 B Yam 2008 GISAID 8 | B/Beijing/184/1993 EPI_ISL_969 B Yam 1993 GISAID 9 | B/Brisbane/1/2008 EPI_ISL_23200 B Yam 2008 GISAID 10 | B/Brisbane/3/2007 EPI_ISL_19933 B Yam 2007 GISAID 11 | B/Brisbane/4/2004 EPI_ISL_12237 B Yam 2004 GISAID 12 | B/Brisbane/5/2004 EPI_ISL_12238 B Yam 2004 GISAID 13 | B/Brisbane/9/2008 EPI_ISL_23837 B Yam 2008 GISAID 14 | B/Bucharest/795/2003 EPI_ISL_2832 B Yam 2003 GISAID 15 | B/Catalonia/S4125/2011 EPI_ISL_99637 B Yam 2011 GISAID 16 | B/Catalonia/S4251/2011 EPI_ISL_101397 B Yam 2011 GISAID 17 | B/Chanthaburi/218/2003 EPI_ISL_7109 B Yam 2003 GISAID 18 | B/Chelyabinsk/306/2007 EPI_ISL_20540 B Yam 2007 GISAID 19 | B/Chongqing/18/2007 EPI_ISL_20479 B Yam 2007 GISAID 20 | B/Colorado/4/2004 EPI_ISL_6590 B Yam 2004 GISAID 21 | B/Dakar/5/2011 EPI_ISL_106886 B Yam 2011 GISAID 22 | B/Dakar/6/2008 EPI_ISL_100278 B Yam 2008 GISAID 23 | B/Dakar/8/2011 EPI_ISL_106887 B Yam 2011 GISAID 24 | B/Egypt/144/2005 EPI_ISL_60848 B Yam 2005 GISAID 25 | B/Ekaterinburg/1/2008 EPI_ISL_23326 B Yam 2008 GISAID 26 | B/England/110/2010 EPI_ISL_98924 B Yam 2010 GISAID 27 | B/England/145/2008 CY115271 B NA 2008 IRD 28 | B/England/170/2010 EPI_ISL_90660 B Yam 2010 GISAID 29 | B/England/23/2004 AJ784059 B NA 2004 IRD 30 | B/England/512/2010 EPI_ISL_90662 B Yam 2010 GISAID 31 | B/Estonia/55669/2011 EPI_ISL_90663 B Yam 2011 GISAID 32 | B/Finland/231/2003 EPI_ISL_4553 B Yam 2003 GISAID 33 | B/Finland/33/2010 EPI_ISL_86993 B Yam 2010 GISAID 34 | B/Finland/39/2010 EPI_ISL_86994 B Yam 2010 GISAID 35 | B/Finland/767/2006 EPI_ISL_21413 B Yam 2006 GISAID 36 | B/Florida/4/2006 EPI_ISL_22808 B Yam 2006 GISAID 37 | B/Florida/7/2004 EPI_ISL_22805 B Yam 2004 GISAID 38 | B/Fujian/430/2004 EPI_ISL_21420 B Yam 2004 GISAID 39 | B/Genoa/12/2002 AY236440 B NA 2002 IRD 40 | B/Genoa/48/2002 AY236450 B NA 2002 IRD 41 | B/Genoa/5/2002 AY236444 B NA 2002 IRD 42 | B/Genoa/56/2002 EPI_ISL_3381 B Yam 2002 GISAID 43 | B/Genova/30/2002 EPI_ISL_2872 B Yam 2002 GISAID 44 | B/Ghana/FS-11-1827/2011 EPI_ISL_103130 B Yam 2011 GISAID 45 | B/Ghana/FS-11-1994/2011 EPI_ISL_103131 B Yam 2011 GISAID 46 | B/Ghana/FS-11-1995/2011 EPI_ISL_103132 B Yam 2011 GISAID 47 | B/Guangdong/120/2000 EPI_ISL_68449 B Yam 2000 GISAID 48 | B/Harbin/7/1994 EPI_ISL_30252 B Yam 1994 GISAID 49 | B/Hebei/19/1994 EPI_ISL_8292 B Vic 1994 GISAID 50 | B/Hebei/3/1994 EPI_ISL_8291 B Vic 1994 GISAID 51 | B/HongKong/1127/2011 EPI_ISL_103119 B Yam 2011 GISAID 52 | B/HongKong/14/1988 EPI_ISL_14764 B Vic 1988 GISAID 53 | B/HongKong/1832/2010 EPI_ISL_79612 B Yam 2010 GISAID 54 | B/HongKong/1895/2010 EPI_ISL_79613 B Yam 2010 GISAID 55 | B/HongKong/2188/2010 EPI_ISL_86995 B Yam 2010 GISAID 56 | B/HongKong/2190/2010 EPI_ISL_86996 B Yam 2010 GISAID 57 | B/HongKong/22/1989 EPI_ISL_6613 B Yam 1989 GISAID 58 | B/HongKong/251/2009 EPI_ISL_70221 B Yam 2009 GISAID 59 | B/HongKong/441/2007 EPI_ISL_20748 B Yam 2007 GISAID 60 | B/HongKong/542/2009 EPI_ISL_70225 B Yam 2009 GISAID 61 | B/Indiana/1/2008 EPI_ISL_23947 B Yam 2008 GISAID 62 | B/Israel/20/2011 EPI_ISL_103323 B Yam 2011 GISAID 63 | B/Jeju/2787/2007 EPI_ISL_20505 B Yam 2007 GISAID 64 | B/Jiangsu/10/2003 CY033844 B NA 2003 IRD 65 | B/Johannesburg/1197/2007 EPI_ISL_20652 B Yam 2007 GISAID 66 | B/Johannesburg/23/2010 EPI_ISL_83772 B Yam 2010 GISAID 67 | B/Johannesburg/40/2010 EPI_ISL_81367 B Yam 2010 GISAID 68 | B/Johannesburg/439/2006 EPI_ISL_13422 B Yam 2006 GISAID 69 | B/Johannesburg/69/2001 EPI_ISL_6812 B Yam 2001 GISAID 70 | B/Johannesburg/90/2007 EPI_ISL_100319 B Yam 2007 GISAID 71 | B/Kadoma/122/1999 EPI_ISL_79 B Yam 1999 GISAID 72 | B/Kadoma/409/2000 EPI_ISL_126 B Yam 2000 GISAID 73 | B/Kadoma/506/1999 EPI_ISL_84 B Yam 1999 GISAID 74 | B/Kobe/1/1994 D38646 B NA 1994 IRD 75 | B/Lisbon/1/2004 EPI_ISL_14087 B Yam 2004 GISAID 76 | B/Lisbon/2/2005 EPI_ISL_14089 B Yam 2005 GISAID 77 | B/Lisbon/3/2005 EPI_ISL_14090 B Yam 2005 GISAID 78 | B/Lusaka/270/1999 EPI_ISL_130 B Yam 1999 GISAID 79 | B/Lusaka/432/1999 EPI_ISL_131 B Yam 1999 GISAID 80 | B/Lyon/1283/2007 EPI_ISL_21543 B Yam 2007 GISAID 81 | B/Macau/131/2004 EPI_ISL_12282 B Yam 2004 GISAID 82 | B/Mashad/6/2009 EPI_ISL_60077 B Yam 2009 GISAID 83 | B/Mauritius/481/2007 EPI_ISL_100292 B Yam 2007 GISAID 84 | B/Mie/1/1993 EPI_ISL_6618 B Yam 1993 GISAID 85 | B/Milano/66/2004 EPI_ISL_2875 B Yam 2004 GISAID 86 | B/NewYork/47/2001 EPI_ISL_3133 B Yam 2001 GISAID 87 | B/Niedersachsen/1/2010 EPI_ISL_85704 B Yam 2010 GISAID 88 | B/Niedersachsen/2/2010 EPI_ISL_87005 B Yam 2010 GISAID 89 | B/NordrheinWestfalen/1/2010 EPI_ISL_87006 B Yam 2010 GISAID 90 | B/Norway/1181/2010 EPI_ISL_86188 B Yam 2010 GISAID 91 | B/Novosibirsk/2/2007 EPI_ISL_20439 B Yam 2007 GISAID 92 | B/Osaka/1201/2000 EPI_ISL_125 B Yam 2000 GISAID 93 | B/Oslo/71/2004 EPI_ISL_2835 B Yam 2004 GISAID 94 | B/Panama/45/1990 EPI_ISL_20945 B Yam 1990 GISAID 95 | B/Paris/1850/2010 EPI_ISL_87007 B Yam 2010 GISAID 96 | B/Paris/1870/2011 EPI_ISL_103134 B Yam 2011 GISAID 97 | B/Paris/1900/2011 EPI_ISL_103135 B Yam 2011 GISAID 98 | B/Parma/5/2002 AJ842085 B NA 2002 IRD 99 | B/Perth/12/2007 EPI_ISL_23135 B Yam 2007 GISAID 100 | B/Perth/204/2008 EPI_ISL_23845 B Yam 2008 GISAID 101 | B/Perth/6/2008 EPI_ISL_23839 B Yam 2008 GISAID 102 | B/Quebec/2/2001 EPI_ISL_2605 B Yam 2001 GISAID 103 | B/Quebec/3/2001 EPI_ISL_2606 B Yam 2001 GISAID 104 | B/Quebec/4/2001 EPI_ISL_2607 B Yam 2001 GISAID 105 | B/Quebec/6/2001 EPI_ISL_2608 B Yam 2001 GISAID 106 | B/Quebec/7/2001 EPI_ISL_2609 B Yam 2001 GISAID 107 | B/Quebec/8/2001 EPI_ISL_2610 B Yam 2001 GISAID 108 | B/Quebec/9/2001 EPI_ISL_2611 B Yam 2001 GISAID 109 | B/Roma/4/2002 EPI_ISL_2878 B Yam 2002 GISAID 110 | B/Sakai/36/2011 EPI_ISL_104040 B Yam 2011 GISAID 111 | B/Santiago/5241/2008 EPI_ISL_23174 B Yam 2008 GISAID 112 | B/Sendai/114/2007 EPI_ISL_20649 B Yam 2007 GISAID 113 | B/Serbia/1894/2011 EPI_ISL_93728 B Yam 2011 GISAID 114 | B/Shanghai/12/1987 EPI_ISL_14762 B Vic 1987 GISAID 115 | B/Shanghai/361/2002 EPI_ISL_2842 B Yam 2002 GISAID 116 | B/Shiga/T30/1998 EPI_ISL_97 B Yam 1998 GISAID 117 | B/Shizuoka/15/2001 EPI_ISL_20974 B Yam 2001 GISAID 118 | B/Sichuan/379/1999 EPI_ISL_21113 B Yam 1999 GISAID 119 | B/Singapore/7/1988 EPI_ISL_14765 B Vic 1988 GISAID 120 | B/Soligorsk/140/2007 EPI_ISL_20513 B Yam 2007 GISAID 121 | B/Stockholm/12/2011 EPI_ISL_90776 B Yam 2011 GISAID 122 | B/Stockholm/4/2009 EPI_ISL_70636 B Yam 2009 GISAID 123 | B/Stockholm/6/2010 EPI_ISL_85688 B Yam 2010 GISAID 124 | B/StPetersburg/94/2008 EPI_ISL_23329 B Yam 2008 GISAID 125 | B/Switzerland/1334249/2008 EPI_ISL_81407 B Yam 2008 GISAID 126 | B/Taiwan/102/2005 EPI_ISL_11201 B Yam 2005 GISAID 127 | B/Taiwan/13/2004 EPI_ISL_11208 B Yam 2004 GISAID 128 | B/Taiwan/142/2005 EPI_ISL_12244 B Yam 2005 GISAID 129 | B/Taiwan/16/2004 EPI_ISL_11221 B Yam 2004 GISAID 130 | B/Taiwan/165/2005 EPI_ISL_11228 B Yam 2005 GISAID 131 | B/Taiwan/34/2004 EPI_ISL_11209 B Yam 2004 GISAID 132 | B/Taiwan/43/2005 EPI_ISL_11202 B Yam 2005 GISAID 133 | B/Taiwan/52/2004 EPI_ISL_11219 B Yam 2004 GISAID 134 | B/Taiwan/54/2004 EPI_ISL_11206 B Yam 2004 GISAID 135 | B/Taiwan/635/2005 EPI_ISL_11213 B Yam 2005 GISAID 136 | B/Taiwan/637/2005 EPI_ISL_21632 B Yam 2005 GISAID 137 | B/Taiwan/68/2004 EPI_ISL_11220 B Yam 2004 GISAID 138 | B/Taiwan/69/2004 EPI_ISL_11207 B Yam 2004 GISAID 139 | B/Taiwan/7/1988 EPI_ISL_14763 B Vic 1988 GISAID 140 | B/Taiwan/79/2006 EPI_ISL_20735 B Yam 2006 GISAID 141 | B/Taiwan/81/2005 EPI_ISL_11212 B Yam 2005 GISAID 142 | B/Taiwan/97271/2001 EPI_ISL_21635 B Yam 2001 GISAID 143 | B/Taiwan/98/2005 EPI_ISL_11211 B Vic 2005 GISAID 144 | B/Tehran/5246/2010 EPI_ISL_85709 B Yam 2010 GISAID 145 | B/Tehran/8/2009 EPI_ISL_60079 B Yam 2009 GISAID 146 | B/Texas/3/2002 EPI_ISL_3134 B Yam 2002 GISAID 147 | B/Texas/6/2011 EPI_ISL_94756 B Yam 2011 GISAID 148 | B/Tokushima/101/1993 EPI_ISL_8289 B Vic 1993 GISAID 149 | B/Tokyo/942/1996 EPI_ISL_975 B Yam 1996 GISAID 150 | B/Tottori/3/2008 EPI_ISL_23477 B Yam 2008 GISAID 151 | B/Trento/3/2002 EPI_ISL_2830 B Yam 2002 GISAID 152 | B/Trieste/23/2005 EPI_ISL_12754 B Yam 2005 GISAID 153 | B/Trieste/7/2002 AY236445 B NA 2002 IRD 154 | B/Turkey/17/2011 EPI_ISL_106875 B Yam 2011 GISAID 155 | B/Turkey/TR-35/2009 EPI_ISL_70238 B Yam 2009 GISAID 156 | B/Turkey/TR-37/2009 EPI_ISL_70239 B Yam 2009 GISAID 157 | B/Ulaanbaatar/1798/2008 CY112231 B NA 2008 IRD 158 | B/Valladolid/18/2008 EPI_ISL_60847 B Yam 2008 GISAID 159 | B/Victoria/508/2004 EPI_ISL_12233 B Yam 2004 GISAID 160 | B/Waikato/1/2006 EPI_ISL_13428 B Yam 2006 GISAID 161 | B/Wisconsin/1/2010 CY115183 B NA 2010 IRD 162 | B/Yamagata/16/1988 EPI_ISL_20958 B Yam 1988 GISAID 163 | B/Yamagata/K298/2001 EPI_ISL_227 B Yam 2001 GISAID 164 | B/Yamagata/K490/2001 EPI_ISL_211 B Yam 2001 GISAID 165 | B/Yamagata/K501/2001 EPI_ISL_213 B Yam 2001 GISAID 166 | B/Yamagata/K508/2001 EPI_ISL_214 B Yam 2001 GISAID 167 | B/Yamagata/K515/2001 EPI_ISL_215 B Yam 2001 GISAID 168 | B/Yamagata/K520/2001 EPI_ISL_217 B Yam 2001 GISAID 169 | B/Yamagata/K521/2001 EPI_ISL_218 B Yam 2001 GISAID 170 | B/Yamagata/K535/2001 EPI_ISL_219 B Yam 2001 GISAID 171 | B/Yamanashi/166/1998 EPI_ISL_20976 B Yam 1998 GISAID 172 | B/Yopougon/GR852/2011 EPI_ISL_103133 B Yam 2011 GISAID 173 | B/Yopougon/GR882/2011 EPI_ISL_103117 B Yam 2011 GISAID 174 | B/Yopougon/GR926/2011 EPI_ISL_103118 B Yam 2011 GISAID 175 | B/Zahedan/7/2009 EPI_ISL_60078 B Yam 2009 GISAID 176 | -------------------------------------------------------------------------------- /example-xmls/H1N1_mds_drift_effects_notree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 207 | 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 | 265 | 266 | 267 | 268 | 269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | -------------------------------------------------------------------------------- /data/Vic_seq_data.tsv: -------------------------------------------------------------------------------- 1 | strain accession type subtype year database 2 | B/Agadir/156/2011 EPI_ISL_99641 B Vic 2011 GISAID 3 | B/Aichi/15/1997 EPI_ISL_32 B Vic 1997 GISAID 4 | B/Aichi/20/1999 EPI_ISL_37 B Vic 1999 GISAID 5 | B/Aichi/3/1998 EPI_ISL_34 B Vic 1998 GISAID 6 | B/Aichi/5/1988 EPI_ISL_1175 B Vic 1988 GISAID 7 | B/AixEnProvence/1795/2011 EPI_ISL_103125 B Vic 2011 GISAID 8 | B/AnnArbor/1/1986 EPI_ISL_10253 B Vic 1986 GISAID 9 | B/Astrakhan/88/2007 EPI_ISL_20541 B Vic 2007 GISAID 10 | B/Bangladesh/5278/2006 EPI_ISL_22467 B Vic 2006 GISAID 11 | B/Barcelona/215/2003 EPI_ISL_2827 B Vic 2003 GISAID 12 | B/Bayern/36/2008 EPI_ISL_32991 B Vic 2008 GISAID 13 | B/Beijing/1/1987 EPI_ISL_2460 B Vic 1987 GISAID 14 | B/Beijing/243/1997 EPI_ISL_970 B Vic 1997 GISAID 15 | B/Belgrade/1094/2009 EPI_ISL_60296 B Vic 2009 GISAID 16 | B/Brazil/2937/2008 EPI_ISL_27661 B Vic 2008 GISAID 17 | B/Brisbane/32/2002 CY018701 B NA 2002 IRD 18 | B/Brisbane/33/2008 EPI_ISL_28588 B Vic 2008 GISAID 19 | B/Brisbane/60/2008 EPI_ISL_28587 B Vic 2008 GISAID 20 | B/Cambodia/30/2011 EPI_ISL_94816 B Vic 2011 GISAID 21 | B/Cheju/303/2003 AJ784058 B NA 2003 IRD 22 | B/Chengdu/54/1988 EPI_ISL_14767 B Vic 1988 GISAID 23 | B/Dakar/31/2002 EPI_ISL_100297 B Vic 2002 GISAID 24 | B/Denmark/16/2011 EPI_ISL_106879 B Vic 2011 GISAID 25 | B/Denmark/21/2011 EPI_ISL_106878 B Vic 2011 GISAID 26 | B/Denmark/22/2011 EPI_ISL_106881 B Vic 2011 GISAID 27 | B/Denmark/23/2011 EPI_ISL_106880 B Vic 2011 GISAID 28 | B/Denmark/24/2011 EPI_ISL_106882 B Vic 2011 GISAID 29 | B/DominicanRepublic/5486/2011 EPI_ISL_104048 B Vic 2011 GISAID 30 | B/Egypt/80/2007 EPI_ISL_100289 B Vic 2007 GISAID 31 | B/England/393/2008 EPI_ISL_60845 B Vic 2008 GISAID 32 | B/Florida/16/2008 EPI_ISL_27675 B Vic 2008 GISAID 33 | B/Fujian/1272/2008 CY115287 B NA 2008 IRD 34 | B/Geneva/5079/2003 AJ784049 B NA 2003 IRD 35 | B/Genoa/33/2002 EPI_ISL_3382 B Vic 2002 GISAID 36 | B/Genoa/55/2002 AY236464 B NA 2002 IRD 37 | B/Genova/2/2002 EPI_ISL_2854 B Vic 2002 GISAID 38 | B/Guangdong/5/1994 EPI_ISL_971 B Vic 1994 GISAID 39 | B/Hawaii/13/2004 EPI_ISL_6591 B Vic 2004 GISAID 40 | B/Hawaii/33/2004 EPI_ISL_22806 B Vic 2004 GISAID 41 | B/Hiroshima/320/2007 EPI_ISL_21443 B Vic 2007 GISAID 42 | B/Hiroshima/9/2010 EPI_ISL_104049 B Vic 2010 GISAID 43 | B/HongKong/1129/2011 EPI_ISL_103120 B Vic 2011 GISAID 44 | B/HongKong/1153/2011 EPI_ISL_103121 B Vic 2011 GISAID 45 | B/HongKong/121/2007 EPI_ISL_20747 B Vic 2007 GISAID 46 | B/HongKong/1351/2002 EPI_ISL_6622 B Vic 2002 GISAID 47 | B/HongKong/1434/2002 EPI_ISL_20955 B Vic 2002 GISAID 48 | B/HongKong/22/2001 EPI_ISL_20952 B Vic 2001 GISAID 49 | B/HongKong/235/2009 EPI_ISL_70223 B Vic 2009 GISAID 50 | B/HongKong/330/2001 EPI_ISL_2342 B Vic 2001 GISAID 51 | B/HongKong/335/2001 EPI_ISL_2343 B Vic 2001 GISAID 52 | B/HongKong/45/2005 EPI_ISL_60843 B Vic 2005 GISAID 53 | B/HongKong/514/2009 EPI_ISL_70224 B Vic 2009 GISAID 54 | B/HongKong/809/2006 EPI_ISL_21494 B Vic 2006 GISAID 55 | B/HongKong/90/2008 EPI_ISL_23156 B Vic 2008 GISAID 56 | B/HongKong/998/2008 EPI_ISL_26192 B Vic 2007 GISAID 57 | B/Hubei/1146/2008 EPI_ISL_23462 B Vic 2008 GISAID 58 | B/Hubei/37/2009 EPI_ISL_33008 B Vic 2009 GISAID 59 | B/Hubei/51/2008 EPI_ISL_29558 B Vic 2008 GISAID 60 | B/Illinois/13/2005 EPI_ISL_21210 B Vic 2005 GISAID 61 | B/India/7600/2001 EPI_ISL_2352 B Vic 2001 GISAID 62 | B/Iwate/17/2009 EPI_ISL_33018 B Vic 2009 GISAID 63 | B/Jiangxi/1792/2007 EPI_ISL_23965 B Vic 2007 GISAID 64 | B/Johannesburg/150/2007 EPI_ISL_20651 B Vic 2007 GISAID 65 | B/Johannesburg/18/2007 EPI_ISL_20672 B Vic 2007 GISAID 66 | B/Johannesburg/27/2005 EPI_ISL_11478 B Vic 2005 GISAID 67 | B/Johannesburg/403/2005 EPI_ISL_100286 B Vic 2005 GISAID 68 | B/Johannesburg/449/2006 EPI_ISL_13423 B Vic 2006 GISAID 69 | B/Johannesburg/508/2006 EPI_ISL_13421 B Vic 2006 GISAID 70 | B/Kagoshima/15/1994 EPI_ISL_8290 B Vic 1994 GISAID 71 | B/Khabarovsk/14/2005 EPI_ISL_21532 B Vic 2005 GISAID 72 | B/Khabarovsk/26/2007 EPI_ISL_20441 B Vic 2007 GISAID 73 | B/Laos/1232/2009 EPI_ISL_71840 B Vic 2009 GISAID 74 | B/Lipetsk/17/2003 EPI_ISL_21541 B Vic 2003 GISAID 75 | B/Lisbon/32/2005 EPI_ISL_14088 B Vic 2005 GISAID 76 | B/Madagascar/2866/2006 EPI_ISL_100281 B Vic 2006 GISAID 77 | B/Madagascar/4254/2009 EPI_ISL_60072 B Vic 2009 GISAID 78 | B/Madagascar/6945/2009 EPI_ISL_70226 B Vic 2009 GISAID 79 | B/Madagascar/7002/2009 EPI_ISL_70233 B Vic 2009 GISAID 80 | B/Malaysia/2506/2004 EU124274 B NA 2004 IRD 81 | B/Malaysia/83077/2001 EPI_ISL_2356 B Vic 2001 GISAID 82 | B/Malta/636714/2011 EPI_ISL_99942 B Vic 2011 GISAID 83 | B/Mauritius/219/2002 EPI_ISL_100303 B Vic 2002 GISAID 84 | B/Mauritius/515/2009 EPI_ISL_60302 B Vic 2009 GISAID 85 | B/Milano/34/2010 EPI_ISL_77010 B Vic 2010 GISAID 86 | B/Milano/36/2010 EPI_ISL_77011 B Vic 2010 GISAID 87 | B/Milano/5/2002 EPI_ISL_2859 B Yam 2002 GISAID 88 | B/Missouri/1/2009 EPI_ISL_29528 B Vic 2009 GISAID 89 | B/Moscow/1/2010 EPI_ISL_77024 B Vic 2010 GISAID 90 | B/Moscow/18/2010 EPI_ISL_77025 B Vic 2010 GISAID 91 | B/Moscow/9/2010 EPI_ISL_77026 B Vic 2010 GISAID 92 | B/Nagasaki/1/1987 EPI_ISL_14746 B Vic 1987 GISAID 93 | B/Nepal/1087/2005 EPI_ISL_10037 B Vic 2005 GISAID 94 | B/Nepal/1090/2005 EPI_ISL_10034 B Vic 2005 GISAID 95 | B/Nepal/1092/2005 EPI_ISL_10033 B Vic 2005 GISAID 96 | B/Nepal/1101/2005 EPI_ISL_10032 B Vic 2005 GISAID 97 | B/Nepal/1118/2005 EPI_ISL_10024 B Vic 2005 GISAID 98 | B/Nepal/1120/2005 EPI_ISL_10023 B Vic 2005 GISAID 99 | B/Nepal/1122/2005 EPI_ISL_10022 B Vic 2005 GISAID 100 | B/Nepal/1131/2005 EPI_ISL_10021 B Vic 2005 GISAID 101 | B/Nepal/1136/2005 EPI_ISL_10019 B Vic 2005 GISAID 102 | B/Nepal/1139/2005 EPI_ISL_10016 B Vic 2005 GISAID 103 | B/Nevada/3/2011 EPI_ISL_104050 B Vic 2011 GISAID 104 | B/NewCaledonia/5/2006 EPI_ISL_13418 B Vic 2006 GISAID 105 | B/NewYork/1/2002 EPI_ISL_2358 B Vic 2002 GISAID 106 | B/Norway/1474/2009 EPI_ISL_60065 B Vic 2009 GISAID 107 | B/Norway/2368/2011 EPI_ISL_103122 B Vic 2011 GISAID 108 | B/Norway/2429/2011 EPI_ISL_103123 B Vic 2011 GISAID 109 | B/Norway/459/2010 EPI_ISL_79600 B Vic 2010 GISAID 110 | B/Odessa/3886/2010 EPI_ISL_77021 B Vic 2010 GISAID 111 | B/Odessa/394/2007 EPI_ISL_20536 B Vic 2007 GISAID 112 | B/Ohio/10/1988 EPI_ISL_14766 B Vic 1988 GISAID 113 | B/Ohio/1/2005 EPI_ISL_99804 B Vic 2005 GISAID 114 | B/Okinawa/10/2009 EPI_ISL_33168 B Vic 2009 GISAID 115 | B/Oman/16296/2001 EPI_ISL_3129 B Vic 2001 GISAID 116 | B/Osaka/16/2007 EPI_ISL_20648 B Vic 2007 GISAID 117 | B/Osaka/491/1997 EPI_ISL_974 B Vic 1997 GISAID 118 | B/Osaka/c19/1993 EPI_ISL_8288 B Vic 1993 GISAID 119 | B/Panama/307237/2010 EPI_ISL_79382 B Vic 2010 GISAID 120 | B/Paris/1762/2009 EPI_ISL_60846 B Vic 2009 GISAID 121 | B/Parma/1/2003 EPI_ISL_2862 B Vic 2003 GISAID 122 | B/Parma/2/2004 EPI_ISL_2865 B Vic 2004 GISAID 123 | B/Parma/28/2002 EPI_ISL_2869 B Vic 2002 GISAID 124 | B/Parma/3/2004 EPI_ISL_2870 B Vic 2004 GISAID 125 | B/Pennsylvania/5/2007 EPI_ISL_15520 B Vic 2007 GISAID 126 | B/Perth/1/2006 EPI_ISL_13410 B Vic 2006 GISAID 127 | B/Perth/14/2006 EPI_ISL_13425 B Vic 2006 GISAID 128 | B/Philippines/1506/2006 EPI_ISL_13426 B Vic 2006 GISAID 129 | B/Philippines/5072/2001 AY139046 B NA 2001 IRD 130 | B/Phitsanulok/2053/2004 EPI_ISL_12240 B Vic 2004 GISAID 131 | B/Roma/1/2003 AJ842074 B NA 2003 IRD 132 | B/Roma/2/2003 AJ842089 B NA 2003 IRD 133 | B/Roma/3/2003 EPI_ISL_2880 B Vic 2003 GISAID 134 | B/Romania/700/2005 EPI_ISL_21586 B Vic 2005 GISAID 135 | B/Sabac/1232/2009 EPI_ISL_60064 B Vic 2009 GISAID 136 | B/Santiago/6025/2011 EPI_ISL_104051 B Vic 2011 GISAID 137 | B/Shandong/7/1997 EPI_ISL_1790 B Vic 1997 GISAID 138 | B/Shanghai/1392/2011 EPI_ISL_94634 B Vic 2011 GISAID 139 | B/Singapore/21/2009 EPI_ISL_60161 B Vic 2009 GISAID 140 | B/Slovakia/1731/2010 EPI_ISL_85706 B Vic 2010 GISAID 141 | B/Stockholm/10/2010 EPI_ISL_85738 B Vic 2010 GISAID 142 | B/Stockholm/1/2010 EPI_ISL_68267 B Vic 2010 GISAID 143 | B/Stockholm/2/2010 EPI_ISL_71846 B Vic 2010 GISAID 144 | B/Stockholm/3/2010 EPI_ISL_75783 B Vic 2010 GISAID 145 | B/Stockholm/5/2010 EPI_ISL_75785 B Vic 2010 GISAID 146 | B/Stockholm/7/2010 EPI_ISL_85689 B Vic 2010 GISAID 147 | B/Stockholm/8/2009 EPI_ISL_68266 B Vic 2009 GISAID 148 | B/Stockholm/9/2010 EPI_ISL_85737 B Vic 2010 GISAID 149 | B/StPetersburg/17/2006 EPI_ISL_21616 B Vic 2006 GISAID 150 | B/Switzerland/5632623/2011 EPI_ISL_106877 B Vic 2011 GISAID 151 | B/Sydney/12/2006 EPI_ISL_13424 B Vic 2006 GISAID 152 | B/Sydney/88/2006 EPI_ISL_13429 B Vic 2006 GISAID 153 | B/Taiwan/11/2010 EPI_ISL_79388 B Vic 2010 GISAID 154 | B/Taiwan/14/2004 EPI_ISL_11198 B Vic 2004 GISAID 155 | B/Taiwan/39/2004 EPI_ISL_11199 B Vic 2004 GISAID 156 | B/Taiwan/61/2004 EPI_ISL_11205 B Vic 2004 GISAID 157 | B/Taiwan/74/2004 EPI_ISL_11203 B Vic 2004 GISAID 158 | B/Taiwan/75/2004 EPI_ISL_11204 B Vic 2004 GISAID 159 | B/Tehran/5277/2010 EPI_ISL_85710 B Vic 2010 GISAID 160 | B/Tehran/80/2002 EPI_ISL_2822 B Vic 2002 GISAID 161 | B/Texas/26/2008 EPI_ISL_28238 B Vic 2008 GISAID 162 | B/Texas/34/2008 EPI_ISL_28262 B Vic 2008 GISAID 163 | B/Texas/37/1988 CY019603 B NA 1988 IRD 164 | B/Texas/39/2006 EPI_ISL_13163 B Vic 2006 GISAID 165 | B/Tokyo/91107/2011 EPI_ISL_103621 B Vic 2011 GISAID 166 | B/Trieste/1/2003 EPI_ISL_12747 B Vic 2003 GISAID 167 | B/Trieste/28/2002 EPI_ISL_2823 B Vic 2002 GISAID 168 | B/Tula/3/2007 EPI_ISL_20444 B Vic 2007 GISAID 169 | B/Turkey/389/2005 EPI_ISL_22486 B Vic 2005 GISAID 170 | B/Uruguay/12/2008 EPI_ISL_23970 B Vic 2008 GISAID 171 | B/Victoria/2/1987 EPI_ISL_6612 B Vic 1987 GISAID 172 | B/Victoria/304/2006 EPI_ISL_60844 B Vic 2006 GISAID 173 | B/Victoria/500/2007 EPI_ISL_23138 B Vic 2007 GISAID 174 | B/Victoria/505/2005 EPI_ISL_12250 B Vic 2005 GISAID 175 | B/Voronezh/20/2011 EPI_ISL_90702 B Vic 2011 GISAID 176 | B/Wellington/1/2006 EPI_ISL_13427 B Vic 2006 GISAID 177 | B/Wellington/85/2006 CY030214 B NA 2006 IRD 178 | B/Wisconsin/27/2008 EPI_ISL_28260 B Vic 2008 GISAID 179 | B/Yamaguchi/1/2010 EPI_ISL_79390 B Vic 2010 GISAID 180 | B/Yunnan/1491/2008 EPI_ISL_29571 B Vic 2008 GISAID 181 | -------------------------------------------------------------------------------- /correspondence/reresponse.tex: -------------------------------------------------------------------------------- 1 | \documentclass[11pt,oneside,letterpaper]{article} 2 | 3 | % graphicx package, useful for including eps and pdf graphics 4 | \usepackage{graphicx} 5 | \DeclareGraphicsExtensions{.pdf,.png,.jpg} 6 | 7 | % basic packages 8 | \usepackage{color} 9 | \usepackage{parskip} 10 | \usepackage{float} 11 | \usepackage{hyperref} 12 | 13 | % text layout 14 | \usepackage{geometry} 15 | \geometry{textwidth=15.25cm} % 15.25cm for single-space, 16.25cm for double-space 16 | \geometry{textheight=22cm} % 22cm for single-space, 22.5cm for double-space 17 | 18 | % helps to keep figures from being orphaned on a page by themselves 19 | \renewcommand{\topfraction}{0.85} 20 | \renewcommand{\textfraction}{0.1} 21 | 22 | % bold the 'Figure #' in the caption and separate it with a period 23 | % Captions will be left justified 24 | \usepackage[labelfont=bf,labelsep=period,font=small]{caption} 25 | 26 | % review layout with double-spacing 27 | %\usepackage{setspace} 28 | %\doublespacing 29 | %\captionsetup{labelfont=bf,labelsep=period,font=doublespacing} 30 | 31 | % cite package, to clean up citations in the main text. Do not remove. 32 | \usepackage{cite} 33 | %\renewcommand\citeleft{(} 34 | %\renewcommand\citeright{)} 35 | %\renewcommand\citeform[1]{\textsl{#1}} 36 | 37 | % Remove brackets from numbering in list of References 38 | \renewcommand\refname{\large References} 39 | \makeatletter 40 | \renewcommand{\@biblabel}[1]{\quad#1.} 41 | \makeatother 42 | 43 | \usepackage{authblk} 44 | \renewcommand\Authands{ \& } 45 | \renewcommand\Authfont{\normalsize \bf} 46 | \renewcommand\Affilfont{\small \normalfont} 47 | \makeatletter 48 | \renewcommand\AB@affilsepx{, \protect\Affilfont} 49 | \makeatother 50 | 51 | % notation 52 | \usepackage{amsmath} 53 | \usepackage{amssymb} 54 | \newcommand{\virus}{\mathbf{x}} % virus coordinate 55 | \newcommand{\serum}{\mathbf{y}} % serum coordinate 56 | \newcommand{\viruses}{\mathbf{X}} % set of virus coordinates 57 | \newcommand{\sera}{\mathbf{Y}} % set of serum coordinates 58 | \newcommand{\ve}{v} % virus effect 59 | \newcommand{\se}{s} % serum effect 60 | \newcommand{\ves}{\mathbf{v}} % set of virus effects 61 | \newcommand{\ses}{\mathbf{s}} % set of serum effects 62 | \newcommand{\point}{f_{\scriptscriptstyle \vert}} % point likelihood 63 | \newcommand{\threshold}{f_{\textstyle \lrcorner}} % threshold likelihood 64 | \newcommand{\interval}{f_{\sqcup}} % interval likelihood 65 | \newcommand{\mdssd}{\varphi} % MDS standard deviation 66 | \newcommand{\virussd}{\sigma_x} % virus / diffusion standard deviation 67 | \newcommand{\serumsd}{\sigma_y} % serum standard deviation 68 | \newcommand{\drift}{\mu} % drift / advection 69 | \newcommand{\tree}{\tau} % phylogeny 70 | \newcommand{\vn}{n} % number of viruses 71 | \newcommand{\sn}{k} % number of sera 72 | \newcommand{\normal}{\mathcal{N}} % normal distribution 73 | \newcommand{\bwithin}{\beta_w} % within clade drift coefficient 74 | \newcommand{\bsister}{\beta_s} % sister clade drift coefficient 75 | \newcommand{\bother}{\beta_t} % across clade drift coefficient 76 | \newcommand{\incclade}[1]{y_\mathrm{#1}} 77 | \newcommand{\driftclade}[1]{x_\mathrm{#1}} 78 | \setlength{\arraycolsep}{2pt} 79 | \newcommand{\smalltwomatrix}[2]{\scriptsize \Big( \begin{matrix} #1 \\ #2 \end{matrix} \Big)} % pretty inline matrix 80 | \newcommand{\smallfourmatrix}[4]{\scriptsize \Big( \begin{matrix} #1 & #2 \\ #3 & #4 \end{matrix} \Big)} % pretty inline matrix 81 | \newcommand{\twomatrix}[2]{\left( \begin{matrix} #1 \\ #2 \end{matrix} \right)} % pretty inline matrix 82 | \newcommand{\fourmatrix}[4]{\left( \begin{matrix} #1 & #2 \\ #3 & #4 \end{matrix} \right)} % pretty inline matrix 83 | 84 | \begin{document} 85 | 86 | \newgeometry{top=4cm} 87 | 88 | Dear eLife editorial board, 89 | 90 | Thank you for conducting a thorough review of our revised manuscript entitled ``Integrating influenza antigenic dynamics with molecular evolution''. We have responded to the remaining reviewer criticisms and believe the manuscript is now suitable for publication in eLife. 91 | 92 | Point-by-point responses follow, as well as a PDF showing revisions that have been made since the last submission. 93 | 94 | Sincerely,\\ 95 | Trevor Bedford 96 | 97 | \restoregeometry 98 | 99 | \newpage 100 | 101 | \section*{Reviewer responses} 102 | 103 | Original reviewer criticisms are in plain text. Our responses follow in \textbf{bold}. 104 | 105 | %%% REREVIEW %%% 106 | \section*{Rereview} 107 | 108 | \subsection*{Main comments} 109 | 110 | I like how the authors have included ``virus effects'' alone in the new Table 1. At least one ``virus effect'' could be overall receptor avidity, and Plotkin and Hensley have a recent paper (Journal of Virology, 87:9904) showing that avidity can influence antigenic clustering. It might be worthwhile to include a sentence on the possibility that ``virus effects'' could be a manifestation of avidity? 111 | 112 | \textbf{We appreciate this suggestion. Including the biological explanation for why we observe virus effects in the form of decreased or increased overall HI reactivity is very important. We've revised this section to include references to virus avidity and relabeled `virus effects' to `virus avidities'. This has the additional benefit of being more transparent of a term than the opaque `effect.'} 113 | 114 | \textbf{With the change from `virus effect' to `virus avidity' made, we chose to make a similar biological realignment of `serum effect' to `serum potency', i.e.\ some sera have higher potency than other other sera, allowing them to inhibit hemagglutination at lower concentrations than other sera. The use of potency here is meant to align with the neutralizing antibody literature which distinguishes neutralization potency from neutralization breadth. Antigenic cartography has not traditionally measured breadth of hemagglutination inhibition.} 115 | 116 | In Table 2 and the related discussion, the authors discuss the scaled effective population size Ne * tau. They never define what tau represents, and I don't think it is safe to assume that the reader will know this -- I certainly don't. More interpretation here would be helpful. 117 | 118 | \textbf{We've revised the manuscript to clarify the definition and interpretation of both $N_e$ and $\tau$.} 119 | 120 | In the ``Punctuated evolution and its epidemiological consequences'' section, the part about subsampling to look at whether drift associates with number of isolates should be expanded. I would suggest starting a new paragraph at the current ``We test to see...'' sentence that briefly explains the rationale for why this test is being done (rationale articulated by other reviewer in original critiques). I also think that it would be nice to have a table or figure somehow representing the actual results of this analysis. 121 | 122 | \textbf{We've expanded out this sentence to a paragraph following the paragraph on the year-to-year drift vs incidence correlation. We give rationale for the test, explain the bootstrap procedure, give $p$-values for both combined and separate analyses across lineages and provide a figure showing a scatterplot of the data.} 123 | 124 | Figure 4 legend refers to ``The mean posterior scaled effective populations... is shown for each virus.'' These are not actually shown in Figure 4, at least not in a way that is obvious to me. 125 | 126 | \textbf{Thank you for catching this. Estimates of $N_e\tau$ had been included in figure 4, but were moved to table 2 and the figure 4 legend not updated accordingly. This has been fixed to leave just the estimates in table 2.} 127 | 128 | My comments where the original reason that the authors removed the argument for the across lineage correlation in incidence. However, now page 11 has this orphan paragraph beginning ``Although the general correlation between rate of antigenic drift...'' This paragraph doesn't seem to make sense in the context of the presented data any more, as the paper no longer has any information about across lineage correlations, so it can't even be seen what they are saying may not be causal. I think this paragraph either needs to be dramatically expended or probably better eliminated. Maybe the previous paragraph could then just get a wrap-up sentence interpreting the results to suggest a strong relationship between drift and incidence within each lineage. 129 | 130 | \textbf{We agree with this advice. We have replaced this paragraph with a wrap-up sentence as suggested.} 131 | 132 | Although the Conclusion is fine, I feel that it might benefit from a paragraph summarizing the main biological results as regards different rates of drift in lineages and the correlation between drift and incidence within lineages. These biological results are not really mentioned in the current Conclusion. 133 | 134 | \textbf{We have revised the Conclusion to include more discussion of biological results.} 135 | 136 | \subsection*{Minor comments} 137 | 138 | The first paragraph of the Introduction refers to ``efficacy against a fixed vaccine formulation to decline over time.'' Although I understand the point, the wording seems off here. What declines is the efficacy of the fixed vaccine formulation against circulating viruses, not the efficacy against the vaccine formulation. 139 | 140 | \textbf{We've revised the clause to ``antigenic drift causes efficacy of a fixed vaccine formulation against circulating viruses to decline over time.''} 141 | 142 | Last sentence of second paragraph of abstract: might be better just to say ``an advantage'' rather than ``a transmission advantage.'' Although drift leads to an advantage that presumably improves R and so in a sense does increase transmission, this advantage probably is acting at the step of viral replication rather than the act of transmission per se. 143 | 144 | \textbf{We agree that ``transmission advantage'' was inexact. This has been revised to the broader ``selective advantage.''} 145 | 146 | Bottom of page 3 says ``of lower of higher dimension.'' The second ``of'' should be an ``or.'' 147 | 148 | \textbf{Fixed.} 149 | 150 | On page 9, ``acribe differences'' should be ``ascribe differences.'' 151 | 152 | \textbf{Fixed.} 153 | 154 | On page 9, the two consecutive sentences beginning ``Previous work using...'' and ``Models of influenza evolution...'' seem slightly redundant. If they are indeed redundant that could be fixed -- if they in fact mean different things, that could be clarified. 155 | 156 | \textbf{We've clarified that the first sentence is referring to general not-necessarily-influenza epidemiological models and the second sentence is referring to influenza-specific models.} 157 | 158 | \end{document} 159 | -------------------------------------------------------------------------------- /example-xmls/README.md: -------------------------------------------------------------------------------- 1 | ## Example XMLs for BMDS cartographic models in BEAST 2 | 3 | ### BEAST 4 | 5 | To run these XMLs [BEAST](http://beast.bio.ed.ac.uk/) will need to be built from the source code. Source code can be found in [Google Code repository](https://code.google.com/p/beast-mcmc/source/checkout). I've set up a [Homebrew formula](https://github.com/Homebrew/homebrew-science/blob/master/beast.rb) to make this easy on Mac. With [Homebrew](http://brew.sh/) installed, just run: 6 | 7 | ``` 8 | brew tap homebrew/science 9 | brew install beast --HEAD 10 | ``` 11 | 12 | ### Data specification 13 | 14 | Titer data should be specified in the following fashion: 15 | 16 | ``` 17 | virusIsolate virusStrain virusYear serumIsolate serumStrain serumYear titer 18 | A/Arizona/14/78 A/Arizona/14/1978 1978 A/Arizona/14/78 A/Arizona/14/1978 1978 640 19 | A/Brazil/11/78 A/Brazil/11/1978 1978 A/Arizona/14/78 A/Arizona/14/1978 1978 160 20 | A/Lackland/3/78 A/Lackland/3/1978 1978 A/Arizona/14/78 A/Arizona/14/1978 1978 160 21 | ... 22 | ``` 23 | 24 | where `virusIsolate` and `serumIsolate` are the unique virus and serum isolates (traditionally rows and columns in an HI table) and `virusStrain` and `serumStrain` are the strains from which these isolates derive. 25 | 26 | The HI data file [`H1N1_HI_data.tsv`](../data/H1N1_HI_data.tsv) is located in the [`data/`](../data/) directory. 27 | 28 | ### Basic model 29 | 30 | The file `H1N1_mds_nodrift_noeffects_notree.xml` gives the most basic cartographic model, corresponding to model #2 in Table 1 of the manuscript. 31 | 32 | The antigenic model is specified by: 33 | 34 | ```xml 35 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | ``` 50 | 51 | Here `mdsDimension` specifies the number of dimensions to use in the BMDS. `intervalWidth` is an optional parameter, that when specified uses interval likelihoods (eq. 7 in the manuscript) rather than point likelihoods (eq. 5 in manuscript). Additionally, there is an optional parameter `mergeSerumIsolates`, that when set to `"true"` takes locations based on `serumStrain` rather than `serumIsolate`. 52 | 53 | MCMC proposals on `virusLocations`, `serumLocations` and `mds.precision` follow: 54 | 55 | ```xml 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | ``` 72 | 73 | Priors on virus and serum locations follow a diffuse normal distribution and prior on `mds.precision` follows a diffuse gamma distribution: 74 | 75 | ```xml 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | ``` 92 | 93 | Virus and serum locations are logged as normal vector parameters: 94 | 95 | ```xml 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | ``` 112 | 113 | ### Drift 114 | 115 | A more complicated model that models antigenic drift is specified in `H1N1_mds_drift_noeffects_notree.xml`. This corresponds to model 6 in Table 1 of the manuscript. 116 | 117 | This differs from the basic model by specifying a positive `location.drift` and specifying `virusOffsets` and `serumOffsets`: 118 | 119 | ```xml 120 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | ``` 144 | 145 | This also requires the addition of: 146 | 147 | ```xml 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | ``` 204 | 205 | Operators include the addition of: 206 | 207 | ```xml 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | ``` 220 | 221 | The diffuse normal prior on virus and serum locations is replaced by hierarchical normal priors: 222 | 223 | ```xml 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | ``` 236 | 237 | And a diffuse gamma prior is included for drift rate: 238 | 239 | ```xml 240 | 241 | 242 | 243 | ``` 244 | 245 | Locations are logged using the *drifted* locations instead of raw locations: 246 | 247 | ```xml 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | ``` 256 | 257 | ### Estimating virus avidity and serum potency 258 | 259 | A more complicated model that includes virus avidity and estimates (rather than fixing) serum potency is specified in `H1N1_mds_drift_effects_notree.xml`. 260 | 261 | This has the addition of: 262 | 263 | ```xml 264 | 265 | 266 | 267 | 268 | 269 | 270 | ``` 271 | 272 | in the `antigenicLikelihood` block. 273 | 274 | And the addition of hierarchical `distributionLikelihoods` on `virusAvidities` and `serumPotencies`: 275 | 276 | ```xml 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | 305 | 306 | 307 | 308 | ``` 309 | 310 | MCMC proposals now include changes to avidity and potency vectors as well as proposals to the hierarchical priors: 311 | 312 | ```xml 313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | ``` 333 | 334 | Notice there is no proposal for `virusAvidities.mean`. This stays fixed at `0.0` for reasons of identifiability. 335 | 336 | Hierarchical priors are included for both virus avidities and serum potencies: 337 | 338 | ```xml 339 | 340 | 341 | 342 | 343 | 344 | 345 | 346 | 347 | 348 | 349 | 350 | 351 | 352 | 353 | 354 | ``` 355 | 356 | Hierarchical parameters are included in the main log file: 357 | 358 | ```xml 359 | 360 | 361 | 362 | 363 | ``` 364 | 365 | and avidities and potencies are recorded in separate log files: 366 | 367 | ```xml 368 | 369 | 370 | 371 | 372 | 373 | 374 | 375 | ``` 376 | 377 | ### Phylogenetic diffusion 378 | 379 | A diffusion model for changes in antigenic phenotype across a viral phylogeny is given in `H1N1_mds_drift_effects_tree.xml`. This corresponds to model 10 in Table 1 of the manuscript. 380 | 381 | This requires the addition of a `taxa` block specifying the year of isolation of a virus and a placeholder for its antigenic location: 382 | 383 | ```xml 384 | 385 | 386 | 387 | 1.0 1.0 388 | 389 | 390 | 391 | 1.0 1.0 392 | 393 | ... 394 | 395 | ``` 396 | 397 | A sequence `alignment` and a `treeLikelihood` model can be included to sample the phylogeny. However, here I'm the simpler approach of running BEAST to generate trees and then using these trees in a downstream BMDS analysis: 398 | 399 | ```xml 400 | 401 | 402 | 403 | 404 | 405 | 406 | 407 | ``` 408 | 409 | The trees input file [`H1N1_sample.trees`](../data/H1N1_sample.trees) is located in the [`data/`](../data/) directory. 410 | 411 | The multivariate diffusion is specified with: 412 | 413 | ```xml 414 | 415 | 416 | 417 | 418 | 419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 | 427 | 428 | 429 | 435 | 436 | 437 | 438 | 439 | 440 | 441 | 442 | 443 | 444 | 445 | 446 | 447 | 448 | 449 | ``` 450 | 451 | The `` block is dropped. 452 | 453 | Operators include: 454 | 455 | ```xml 456 | 457 | 458 | 459 | ``` 460 | 461 | and the operator on `virus.precision` is replaced with: 462 | 463 | ```xml 464 | 465 | 466 | 467 | ``` 468 | 469 | Priors include: 470 | 471 | ```xml 472 | 473 | 474 | 475 | 476 | 477 | ``` 478 | 479 | The location-tagged phylogeny is logged with: 480 | 481 | ```xml 482 | 483 | 484 | 485 | 486 | 487 | 488 | 489 | 490 | ``` 491 | 492 | ## Other subtypes 493 | 494 | Full analysis files for H3N2, B/Vic and B/Yam, corresponding to the `mds_drift_effects_tree` model are also provided here: 495 | 496 | * [`H3N2_mds_drift_effects_tree.xml`](H3N2_mds_drift_effects_tree.xml) 497 | * [`Vic_mds_drift_effects_tree.xml`](Vic_mds_drift_effects_tree.xml) 498 | * [`Yam_mds_drift_effects_tree.xml`](Yam_mds_drift_effects_tree.xml) 499 | 500 | Data files for trees and HI titers for these also reside in the [`data/`](../data/) directory. -------------------------------------------------------------------------------- /figure-data/fig09_smith_mds.tsv: -------------------------------------------------------------------------------- 1 | type name year ag1 ag2 potency 2 | virus A/Rotterdam/577/1980 1980. -6.9832 -3.9938 na 3 | virus A/ChristChurch/2/1988 1988. -2.8774 -3.87 na 4 | virus A/Netherlands/241/1993 1993. 4.7033 3.9962 na 5 | virus A/HongKong/55/1994 1994. 5.5412 3.2813 na 6 | virus A/England/7/1994 1994. 7.9809 2.12 na 7 | virus A/Johannesburg/33/1994 1994. 5.798 6.4639 na 8 | virus A/Johannesburg/47/1994 1994. 3.3392 6.3114 na 9 | virus A/Netherlands/1/1995 1995. 5.1528 4.9152 na 10 | virus A/HongKong/32/1995 1995. 4.6899 3.9348 na 11 | virus A/Bilthoven/15793/1968 1968. -15.0344 3.5187 na 12 | virus A/Bilthoven/16190/1968 1968. -15.6443 4.3512 na 13 | virus A/Bilthoven/16398/1968 1968. -13.8236 3.9902 na 14 | virus A/HongKong/1/1968 1968. -15.4266 4.9187 na 15 | virus A/Bilthoven/808/1969 1969. -14.7866 2.9006 na 16 | virus A/Bilthoven/908/1969 1969. -14.2916 4.5925 na 17 | virus A/Bilthoven/17938/1969 1969. -14.5 5.15 na 18 | virus A/Bilthoven/93/1970 1970. -14.8388 3.3857 na 19 | virus A/Bilthoven/2668/1970 1970. -14.7351 5.6603 na 20 | virus A/Bilthoven/6449/1971 1971. -13.6064 7.4097 na 21 | virus A/Bilthoven/21438/1971 1971. -12.6025 5.1844 na 22 | virus A/Bilthoven/21801/1971 1971. -15.8004 3.9075 na 23 | virus A/HongKong/107/1971 1971. -16.7535 1.8582 na 24 | virus A/Bilthoven/6022/1972 1972. -14.6817 3.2124 na 25 | virus A/Bilthoven/21793/1972 1972. -13.8775 2.2432 na 26 | virus A/Bilthoven/23290/1972 1972. -14.8064 1.7561 na 27 | virus A/Bilthoven/23337/1972 1972. -14.0315 1.7361 na 28 | virus A/England/42/1972 1972. -14.6437 2.941 na 29 | virus A/Bilthoven/552/1973 1973. -12.966 0.8634 na 30 | virus A/Bilthoven/748/1973 1973. -13.8354 0.9588 na 31 | virus A/Bilthoven/3517/1973 1973. -12.6836 1.7044 na 32 | virus A/PortChalmers/1/1973 1973. -12.7455 1.4446 na 33 | virus A/Bilthoven/5146/1974 1974. -13.8367 0.0606 na 34 | virus A/Bilthoven/5930/1974 1974. -13.661 1.8368 na 35 | virus A/Bilthoven/5931/1974 1974. -11.2954 2.5188 na 36 | virus A/Bilthoven/7398/1974 1974. -14.4473 -0.6409 na 37 | virus A/Bilthoven/9459/1974 1974. -12.4934 0.997 na 38 | virus A/Bilthoven/4273/1975 1975. -13.9766 -0.4407 na 39 | virus A/Bilthoven/334/1975 1975. -13.7128 0.1566 na 40 | virus A/Bilthoven/1843/1975 1975. -14.3795 0.3813 na 41 | virus A/Bilthoven/2600/1975 1975. -13.7874 0.1313 na 42 | virus A/Bilthoven/2813/1975 1975. -14.5879 1.146 na 43 | virus A/Victoria/3/1975 1975. -10.1599 0.3171 na 44 | virus A/Bilthoven/5168/1976 1976. -9.8486 0.6871 na 45 | virus A/Bilthoven/628/1976 1976. -8.6911 -1.9065 na 46 | virus A/Bilthoven/1761/1976 1976. -8.7059 1.0858 na 47 | virus A/Bilthoven/2271/1976 1976. -8.8909 -1.0016 na 48 | virus A/Bilthoven/5029/1976 1976. -7.5275 1.3168 na 49 | virus A/Bilthoven/5657/1976 1976. -8.6728 0.9025 na 50 | virus A/Bilthoven/6545/1976 1976. -8.4251 0.8957 na 51 | virus A/Amsterdam/1609/1977 1977. -9.7263 0.6462 na 52 | virus A/Bilthoven/3895/1977 1977. -8.9381 0.9222 na 53 | virus A/Rotterdam/5828/1977 1977. -10.1033 1.0587 na 54 | virus A/Rotterdam/8179/1977 1977. -9.1714 1.0924 na 55 | virus A/Texas/1/1977 1977. -8.8176 -4.6857 na 56 | virus A/Bangkok/1/1979 1979. -7.8474 -6.3617 na 57 | virus A/Netherlands/209/1980 1980. -7.0846 -3.3708 na 58 | virus A/Lyon/2380/1981 1981. -6.0402 -3.7894 na 59 | virus A/Bilthoven/4791/1981 1981. -6.3262 -2.7049 na 60 | virus A/Netherlands/233/1982 1982. -6.6852 -3.4371 na 61 | virus A/Netherlands/241/1982 1982. -6.6073 -3.3112 na 62 | virus A/Bilthoven/10684/1982 1982. -6.6869 -3.6243 na 63 | virus A/Philippines/2/1982 1982. -5.8714 -5.751 na 64 | virus A/Oslow/13676/1983 1983. -5.5592 -4.0542 na 65 | virus A/Caen/1/1984 1984. -5.3707 -1.4071 na 66 | virus A/Netherlands/330/1985 1985. -5.2821 -2.7391 na 67 | virus A/Stockholm/10/1985 1985. -5.1465 -2.1781 na 68 | virus A/Wellington/4/1985 1985. -4.582 -2.0403 na 69 | virus A/Netherlands/333/1985 1985. -5.2611 -1.0325 na 70 | virus A/Guildford/V728/1985 1985. -3.5442 -3.0442 na 71 | virus A/Colorado/2/1986 1986. -5.0654 -3.6183 na 72 | virus A/Leningrad/360/1986 1986. -3.4496 -5.4414 na 73 | virus A/Sichuan/2/1987 1987. -4.2543 1.7538 na 74 | virus A/Victoria/7/1987 1987. -1.2127 -2.8102 na 75 | virus A/Shanghai/11/1987 1987. -2.7725 1.5917 na 76 | virus A/Netherlands/450/1988 1988. -1.7174 -0.9312 na 77 | virus A/Victoria/1/1988 1988. -0.8392 -3.3725 na 78 | virus A/Stockholm/12/1988 1988. -3.4993 -0.5254 na 79 | virus A/England/427/1988 1988. -1.8152 -1.0101 na 80 | virus A/Netherlands/620/1989 1989. -2.0708 -0.0055 na 81 | virus A/England//1989 1989. -2.6334 -0.5583 na 82 | virus A/Geneva/5007/1989 1989. -1.8118 -0.3332 na 83 | virus A/Guizhou/54/1989 1989. -2.1245 2.078 na 84 | virus A/HongKong/1/1989 1989. -2.2008 -1.1485 na 85 | virus A/Netherlands/650/1989 1989. -2.7978 1.2085 na 86 | virus A/Netherlands/738/1989 1989. -4.7458 1.9932 na 87 | virus A/Singapore/35/1989 1989. -2.2279 -0.2992 na 88 | virus A/Singapore/40/1989 1989. -0.9513 -1.4777 na 89 | virus A/Wellington/5/1989 1989. -3.5559 1.5965 na 90 | virus A/Beijing/353/1989 1989. 0.697 -3.9852 na 91 | virus A/Beijing/352/1989 1989. 1.4162 -0.2708 na 92 | virus A/Atlanta/211/1989 1989. -1.561 -1.273 na 93 | virus A/Singapore/34/1989 1989. 0.0297 -1.549 na 94 | virus A/Singapore/36/1989 1989. -0.8416 1.1848 na 95 | virus A/Singapore/53/1989 1989. -0.9826 -2.2712 na 96 | virus A/Victoria/1/1989 1989. -5.0961 1.791 na 97 | virus A/Victoria/2/1990 1990. 1.0638 -2.9877 na 98 | virus A/Wellington/3/1990 1990. 1.6858 -2.1568 na 99 | virus A/Memphis/2/1990 1990. -2.7303 0.3299 na 100 | virus A/Seoul/1/1990 1990. -2.5252 0.051 na 101 | virus A/Memphis/5/1990 1990. -1.9685 -3.5503 na 102 | virus A/Shanghai/24/1990 1990. -0.4848 2.2981 na 103 | virus A/Lyon/1149/1991 1991. 2.4231 -1.2304 na 104 | virus A/Netherlands/891/1991 1991. 0.6049 -2.4356 na 105 | virus A/Canberra/1/1991 1991. -2.6096 -1.8477 na 106 | virus A/England/260/1991 1991. -0.0054 -2.7872 na 107 | virus A/England/261/1991 1991. 2.5645 -0.4991 na 108 | virus A/Madrid/G12/1991 1991. 0.4498 -2.4675 na 109 | virus A/Netherlands/816/1991 1991. 0.3408 -2.8687 na 110 | virus A/Geneva/5366/1991 1991. -1.8768 0.3525 na 111 | virus A/Lyon/1182/1991 1991. 2.0711 -1.956 na 112 | virus A/Geneva/6447/1991 1991. 2.1905 -3.0224 na 113 | virus A/Lyon/1189/1991 1991. 1.2415 -2.7703 na 114 | virus A/Lyon/1276/1991 1991. 3.2995 -1.972 na 115 | virus A/Lyon/1337/1991 1991. 1.3866 -0.5641 na 116 | virus A/Lyon/1373/1991 1991. 1.6796 -2.8668 na 117 | virus A/Lyon/1594/1991 1991. 1.3151 -3.3789 na 118 | virus A/Lyon/23672/1991 1991. 1.4616 -4.6568 na 119 | virus A/Lyon/24103/1991 1991. 0.2726 -3.434 na 120 | virus A/Lyon/24222/1991 1991. 1.7974 -2.1227 na 121 | virus A/Stockholm/20/1991 1991. 1.1073 -2.6791 na 122 | virus A/Victoria/33/1992 1992. -0.1061 -1.5286 na 123 | virus A/Amsterdam/4112/1992 1992. 1.0785 -2.347 na 124 | virus A/Enschede/1285/1992 1992. 0.8276 -3.4494 na 125 | virus A/Finland/220/1992 1992. 2.1722 -2.8782 na 126 | virus A/Madrid/G58/1992 1992. 1.9375 -3.0207 na 127 | virus A/Nijmegen/3129/1992 1992. 0.9596 -2.7267 na 128 | virus A/Netherlands/819/1992 1992. 1.3341 -2.1344 na 129 | virus A/Netherlands/935/1992 1992. 0.6563 -2.596 na 130 | virus A/Paris/583/1992 1992. 0.4218 -4.1481 na 131 | virus A/Paris/614/1992 1992. 0.7031 -3.3024 na 132 | virus A/SouthAustralia/8/1992 1992. 1.4956 -4.7057 na 133 | virus A/SouthAustralia/23/1992 1992. 1.2782 -4.6303 na 134 | virus A/SouthAustralia/27/1992 1992. 3.0586 -3.2262 na 135 | virus A/Stockholm/7/1992 1992. 0.4327 -4.6127 na 136 | virus A/Victoria/68/1992 1992. 0.9324 -2.0268 na 137 | virus A/Paris/467/1992 1992. 0.296 -2.6273 na 138 | virus A/Tilburg/5957/1992 1992. 0.958 -3.0517 na 139 | virus A/Beijing/32/1992 1992. 0.6848 3.9704 na 140 | virus A/Finland/247/1992 1992. 3.8302 4.5809 na 141 | virus A/Netherlands/938/1992 1992. 0.526 3.212 na 142 | virus A/Sendai/C273/1992 1992. 2.2067 6.3031 na 143 | virus A/Stockholm/12/1992 1992. 3.1704 3.347 na 144 | virus A/Stockholm/13/1992 1992. 0.6367 -2.0088 na 145 | virus A/Umea/1982/1992 1992. 2.5098 -0.2596 na 146 | virus A/Umea/2000/1992 1992. 1.5476 -2.4819 na 147 | virus A/Finland/218/1992 1992. 2.3194 -4.1238 na 148 | virus A/Geneva/5113/1992 1992. 1.0412 -4.3222 na 149 | virus A/Houston/56798/1992 1992. 1.698 -3.765 na 150 | virus A/Houston/56829/1992 1992. 1.4548 -2.5486 na 151 | virus A/Houston/56941/1992 1992. 1.9921 -3.2372 na 152 | virus A/Nijmegen/3126/1992 1992. 0.7541 -3.3625 na 153 | virus A/Netherlands/823/1992 1992. 1.5618 -2.3045 na 154 | virus A/Paris/320/1992 1992. 0.6408 -3.2305 na 155 | virus A/Paris/325/1992 1992. 0.8679 -3.1415 na 156 | virus A/Paris/407/1992 1992. 0.2152 -4.4882 na 157 | virus A/Paris/417/1992 1992. 2.0212 -1.1742 na 158 | virus A/Paris/424/1992 1992. 1.6403 -3.4207 na 159 | virus A/Paris/457/1992 1992. -1.0491 -5.1684 na 160 | virus A/Paris/490/1992 1992. 1.4929 -2.684 na 161 | virus A/Paris/512/1992 1992. 2.1329 -4.7638 na 162 | virus A/Paris/548/1992 1992. 0.5511 -4.8643 na 163 | virus A/Paris/564/1992 1992. 2.3269 -2.1905 na 164 | virus A/Paris/597/1992 1992. 2.7171 -3.0632 na 165 | virus A/Rotterdam/100540/1992 1992. 1.0885 -3.1364 na 166 | virus A/Stockholm/8/1992 1992. 2.2567 -1.9736 na 167 | virus A/Madrid/G102/1993 1993. 3.5514 3.673 na 168 | virus A/Madrid/G252/1993 1993. 6.5712 1.1168 na 169 | virus A/Akita/4/1993 1993. 3.9392 5.7807 na 170 | virus A/Enschede/5458/1993 1993. 2.8713 -1.1203 na 171 | virus A/Madrid/G101/1993 1993. 0.7528 -2.4825 na 172 | virus A/Madrid/G109/1993 1993. 3.8779 3.6221 na 173 | virus A/Madrid/G116/1993 1993. 2.4217 -2.4046 na 174 | virus A/Madrid/G122/1993 1993. 4.2045 3.9553 na 175 | virus A/Madrid/G130/1993 1993. 0.9911 4.0325 na 176 | virus A/Netherlands/3/1993 1993. 3.3181 1.4855 na 177 | virus A/Netherlands/17/1993 1993. 1.7396 2.7385 na 178 | virus A/Netherlands/101/1993 1993. 0.6665 4.6401 na 179 | virus A/Netherlands/115/1993 1993. 1.8088 4.7498 na 180 | virus A/Netherlands/126/1993 1993. 0.9845 5.7067 na 181 | virus A/Netherlands/165/1993 1993. 1.8316 -4.0811 na 182 | virus A/Netherlands/179/1993 1993. 2.4158 2.8126 na 183 | virus A/Paris/287/1993 1993. 2.8328 -2.1767 na 184 | virus A/Shiga/6/1993 1993. 4.1383 6.6474 na 185 | virus A/Yamagata/56/1993 1993. 3.6574 5.7953 na 186 | virus A/Yamagata/61/1993 1993. 2.1479 7.3108 na 187 | virus A/Yamagata/62/1993 1993. 3.2408 6.668 na 188 | virus A/Netherlands/399/1993 1993. 5.5486 0.3158 na 189 | virus A/Shangdong/9/1993 1993. 3.4816 6.1842 na 190 | virus A/Lyon/672/1993 1993. 3.485 4.4641 na 191 | virus A/Lyon/1803/1993 1993. 3.7288 4.0134 na 192 | virus A/Netherlands/357/1993 1993. 3.5255 3.7203 na 193 | virus A/Netherlands/371/1993 1993. 3.7078 5.0521 na 194 | virus A/Netherlands/372/1993 1993. 6.678 0.4907 na 195 | virus A/Netherlands/398/1993 1993. 3.8743 3.5956 na 196 | virus A/Netherlands/440/1993 1993. 2.396 3.8183 na 197 | virus A/Oslow/2219/1993 1993. 4.221 3.3013 na 198 | virus A/Oslow/2352/1993 1993. 2.2608 4.71 na 199 | virus A/Stockholm/20/1993 1993. 4.765 2.8056 na 200 | virus A/Victoria/104/1993 1993. 4.1446 3.9577 na 201 | virus A/Wellington/59/1993 1993. 4.1082 5.4279 na 202 | virus A/Singapore/19/1993 1993. 5.7076 0.6494 na 203 | virus A/Lyon/1815/1993 1993. 4.9377 3.3463 na 204 | virus A/Lyon/22686/1993 1993. 3.232 5.1448 na 205 | virus A/Lyon/23602/1993 1993. 4.5602 3.1653 na 206 | virus A/Singapore/3/1993 1993. 2.0208 4.0296 na 207 | virus A/Guangdong/25/1993 1993. 3.882 5.781 na 208 | virus A/Scotland/142/1993 1993. 2.4122 2.2107 na 209 | virus A/Scotland/160/1993 1993. 5.0244 4.7304 na 210 | virus A/HongKong/1/1994 1994. 4.7299 3.9962 na 211 | virus A/HongKong/2/1994 1994. 3.9498 3.1362 na 212 | virus A/HongKong/56/1994 1994. 5.3443 3.8142 na 213 | virus A/SouthAustralia/15/1994 1994. 5.3642 3.5456 na 214 | virus A/SouthAustralia/25/1994 1994. 5.082 4.1432 na 215 | virus A/Netherlands/18/1994 1994. 5.0781 2.8201 na 216 | virus A/Finland/338/1995 1995. 6.0416 1.4068 na 217 | virus A/Stockholm/506/1995 1995. 4.8861 2.5075 na 218 | virus A/Geneva/AI9509/1995 1995. 5.1631 1.2154 na 219 | virus A/Finland/339/1995 1995. 7.9865 1.3284 na 220 | virus A/HongKong/3/1995 1995. 4.9509 2.9324 na 221 | virus A/Finland/381/1995 1995. 8.9162 4.0402 na 222 | virus A/HongKong/38/1995 1995. 5.2532 2.9522 na 223 | virus A/HongKong/49/1995 1995. 6.676 1.78 na 224 | virus A/HongKong/55/1995 1995. 5.5173 1.4742 na 225 | virus A/Lyon/2279/1995 1995. 4.9709 1.5044 na 226 | virus A/Nanchang/933/1995 1995. 5.6593 0.9669 na 227 | virus A/Netherlands/271/1995 1995. 8.5537 2.2435 na 228 | virus A/Victoria/75/1995 1995. 4.3358 2.2271 na 229 | virus A/Wuhan/359/1995 1995. 6.2154 -0.5018 na 230 | virus A/Brisbane/8/1996 1996. 5.9507 -0.8045 na 231 | virus A/Geneva/3958/1996 1996. 6.5691 0.7933 na 232 | virus A/HongKong/20/1996 1996. 6.8662 0.4992 na 233 | virus A/HongKong/42/1996 1996. 4.6955 4.3356 na 234 | virus A/HongKong/357/1996 1996. 6.1271 0.79 na 235 | virus A/HongKong/358/1996 1996. 6.0087 -0.2912 na 236 | virus A/HongKong/434/1996 1996. 4.5749 6.4782 na 237 | virus A/Netherlands/91/1996 1996. 4.1413 4.269 na 238 | virus A/Singapore/1/1996 1996. 5.6883 0.0843 na 239 | virus A/Lyon/1781/1996 1996. 6.268 1.0019 na 240 | virus A/HongKong/1/1997 1997. 5.9768 -0.6892 na 241 | virus A/Nice/491/1997 1997. 7.6635 -0.663 na 242 | virus A/Auckland/10/1997 1997. 9.2453 -3.2228 na 243 | virus A/HongKong/280/1997 1997. 7.819 -0.053 na 244 | virus A/Netherlands/300/1997 1997. 9.3413 -2.8529 na 245 | virus A/Sydney/5/1997 1997. 10.4832 -3.2111 na 246 | virus A/Johannesburg/10/1997 1997. 5.3492 -0.3284 na 247 | virus A/Oslow/21/1997 1997. 7.2799 -0.1298 na 248 | virus A/Oslow/244/1997 1997. 5.1646 -0.0274 na 249 | virus A/Netherlands/5/1998 1998. 5.8044 0.2778 na 250 | virus A/Netherlands/414/1998 1998. 9.5578 -1.8692 na 251 | virus A/Netherlands/462/1998 1998. 9.7415 -2.7675 na 252 | virus A/Netherlands/427/1998 1998. 10.6708 -2.7075 na 253 | virus A/Moscow/10/1999 1999. 8.5736 -3.2862 na 254 | virus A/Netherlands/301/1999 1999. 10.5695 -2.7728 na 255 | virus A/Panama/2007/1999 1999. 10.0462 -1.3185 na 256 | virus A/Netherlands/3/2000 2000. 11.319 -0.97 na 257 | virus A/Netherlands/118/2001 2001. 10.7213 -2.1411 na 258 | virus A/Netherlands/126/2001 2001. 11.5352 -0.9057 na 259 | virus A/Netherlands/124/2001 2001. 11.5075 -1.6175 na 260 | virus A/Netherlands/1/2002 2002. 12.2592 0.5111 na 261 | virus A/Netherlands/120/2002 2002. 9.7239 -1.7179 na 262 | virus A/Fujian/411/2002 2002. 15.6149 -2.1654 na 263 | virus A/Netherlands/22/2003 2003. 14.3527 1.2986 na 264 | virus A/Netherlands/213/2003 2003. 13.0992 -1.8003 na 265 | virus A/Netherlands/217/2003 2003. 14.3415 -1.6546 na 266 | virus A/Netherlands/222/2003 2003. 13.8108 -1.0375 na 267 | virus A/Finland/170/2003 2003. 13.5403 -0.6427 na 268 | virus A/Netherlands/20/2003 2003. 10.5199 -0.7477 na 269 | virus AL/4382/82 1982. -5.7821 -4.1453 na 270 | virus OK/5/88 1988. -1.1485 -4.1746 na 271 | virus AT/3572DASH5/88 1988. -2.8603 -2.1064 na 272 | virus EI/3447/89 1989. -2.0395 -0.122 na 273 | virus WK/1/89 1989. -2.7217 0.4616 na 274 | virus OV/31/92 1992. -0.2213 -2.4825 na 275 | serum CC/4/85 1985. -6.6066 -3.1901 10.1293 276 | serum NL/330/85 1985. -5.1178 -2.1625 11.3219 277 | serum NL/450/88 1988. -2.5695 -1.0277 13.3219 278 | serum WE/4/85 1985. -3.7217 -1.9598 12.3219 279 | serum PR/413/94 1994. 5.287 3.6211 11.3219 280 | serum TE/1A/77 1977. -8.5129 -2.9076 10.9887 281 | serum PH/2/82 1982. -5.9178 -5.2068 12.3219 282 | serum VI/7/87 1987. -1.6669 -1.8335 11.3219 283 | serum SI/2/87 1987. -3.542 -0.3164 11.9887 284 | serum EN/496/80 1980. -6.6884 -4.939 12.3219 285 | serum HK/1/68 1968. -14.7642 5.382 10.3219 286 | serum EN/42/72 1972. -12.3684 3.7102 12.3219 287 | serum PC/1/73 1973. -12.3422 0.5667 11.3219 288 | serum VI/3A/75 1975. -9.7302 2.0733 11.3219 289 | serum LE/360/86 1986. -5.7577 -2.8024 11.3219 290 | serum BA/1/79 1979. -6.7276 -6.1474 10.3219 291 | serum SL/840/74 1974. -13.9615 -1.1186 11.3219 292 | serum BI/21793/72 1972. -13.8746 2.9811 10.3219 293 | serum BI/5930/74 1974. -12.7218 1.1645 10.3219 294 | serum AM/1609/77 1977. -7.1933 0.6047 11.3219 295 | serum BI/2461/78 1978. -6.7804 -4.9645 11.8218 296 | serum RD/577/80 1980. -6.5364 -5.7746 12.3219 297 | serum NL/209/80 1980. -8.0175 -5.3151 12.3219 298 | serum NL/233/82 1982. -7.7031 -4.2649 11.3219 299 | serum NL/241/82 1982. -7.6491 -4.8071 12.3219 300 | serum ST/10/85 1985. -4.4762 -1.8144 11.8218 301 | serum VI/2/90 1990. 0.2846 -3.2079 12.3219 302 | serum LY/1149/91 1991. 1.993 -1.7716 11.3219 303 | serum MA/G252/93 1993. 5.5256 2.4034 10.0715 304 | serum NL/1/95 1995. 5.8101 5.3582 12.3219 305 | serum NL/218/95 1995. 6.2774 4.2941 11.7065 306 | serum NL/172/96 1996. 7.2482 1.2151 11.3219 307 | serum TE/1B/77 1977. -8.4987 -3.3213 13.3219 308 | serum BA/2/79 1979. -5.7199 -3.2146 11.3219 309 | serum CE/1B/84 1984. -4.6714 -2.3197 9.3219 310 | serum CO/2/86 1986. -3.3926 -2.8248 13.3219 311 | serum BE/353/89 1989. 0.6164 -1.1912 12.3219 312 | serum VI/3C/75 1975. -9.3627 -0.4278 11.3219 313 | serum SH/11/87 1987. -3.4604 0.2924 13.3219 314 | serum GD/25/93 1993. 6.5072 6.0006 12.9069 315 | serum JO/33/94 1994. 6.3727 5.3059 12.9069 316 | serum NL/47/95 1995. 6.5675 2.7321 10.9069 317 | serum NA/933/95 1995. 8.395 1.009 10.3219 318 | serum LY/2279/95 1995. 7.5796 2.9057 12.1293 319 | serum SP/1/96 1996. 6.1296 -0.8742 11.5718 320 | serum AU/10/97 1997. 9.1 -1.8309 12.1144 321 | serum NL/5/98 1998. 7.8084 1.3966 12.3219 322 | serum NL/18/94 1994. 8.0835 2.4826 11.9069 323 | serum HK/107/71 1971. -18.9282 1.1005 12.3219 324 | serum PH/2V/82 1982. -7.6652 -3.6228 11.2761 325 | serum BE/32V/92 1992. 1.1627 3.6504 10.0941 326 | serum NL/286/97 1997. 6.179 0.5607 9.9069 327 | serum SY/5V/97 1997. 10.4148 -4.3148 12.9069 328 | serum GU/54/89 1989. -2.3495 0.7867 13.3219 329 | serum NL/333/85 1985. -6.7624 -2.9075 10.3219 330 | serum CE/1A/84 1984. -6.2874 -2.8858 10.3219 331 | serum SH/31/80 1980. -6.4253 -3.6622 9.9069 332 | serum NL/620/89 1989. -1.6585 -1.1243 14.3219 333 | serum BE/32A/92 1992. 3.1631 2.8129 10.4828 334 | serum HK/34/90 1990. -0.2367 2.0175 13.3219 335 | serum BE/32B/92 1992. 2.4584 2.5534 9.8218 336 | serum FI/338/95 1995. 6.5944 3.9117 13.3219 337 | serum SD/9/93 1993. 3.74 3.8276 12.1293 338 | serum OS/2352/93 1993. 3.5886 4.3773 10.8796 339 | serum GE/A9509/95 1995. 5.1019 3.0432 11.4681 340 | serum BR/8/96 1996. 7.0603 0.799 11.5718 341 | serum SY/5B/97 1997. 8.282 -3.5514 12.9069 342 | serum SY/5A/97 1997. 9.6055 -2.4232 11.9894 343 | serum WU/359B/95 1995. 7.8853 0.6036 11.3219 344 | serum MW/10/99 1999. 10.8823 -2.1563 11.7752 345 | serum SY/5HAY/97 1997. 11.7629 -2.2829 11.9069 346 | serum NL/1/02 2002. 9.5869 -1.1865 11.3219 347 | serum PM/2007/99 1999. 11.9555 -1.9005 11.7258 348 | serum NL/126/01 2001. 10.9869 -1.7737 11.3219 349 | serum NL/118/01 2001. 10.7199 -1.6601 11.5182 350 | serum FU/411/02 2002. 14.9851 -0.3846 12.9885 351 | serum NL/88/03 2003. 11.4371 -1.3297 11.9069 352 | serum NL/22/03 2003. 14.0698 -1.7521 12.5365 353 | serum NL/124/01 2001. 11.6492 -2.6414 11.9069 -------------------------------------------------------------------------------- /figure-data/fig10_smith_mds_rotation.tsv: -------------------------------------------------------------------------------- 1 | type name year ag1 ag2 potency 2 | virus A/Rotterdam/577/1980 1980. -7.3544 3.3986 na 3 | virus A/ChristChurch/2/1988 1988. -4.2422 2.2046 na 4 | virus A/Netherlands/241/1993 1993. 6.5456 1.9834 na 5 | virus A/HongKong/55/1994 1994. 6.5543 0.2947 na 6 | virus A/England/7/1994 1994. 8.0402 -1.9307 na 7 | virus A/Johannesburg/33/1994 1994. 8.3694 3.5829 na 8 | virus A/Johannesburg/47/1994 1994. 7.937 3.9345 na 9 | virus A/Netherlands/1/1995 1995. 7.1661 2.1162 na 10 | virus A/HongKong/32/1995 1995. 6.8289 2.229 na 11 | virus A/Bilthoven/15793/1968 1968. -15.2107 -1.4019 na 12 | virus A/Bilthoven/16190/1968 1968. -13.8742 -5.0978 na 13 | virus A/Bilthoven/16398/1968 1968. -14.0897 -3.9896 na 14 | virus A/HongKong/1/1968 1968. -15.4146 -4.1429 na 15 | virus A/Bilthoven/808/1969 1969. -13.5232 -5.9893 na 16 | virus A/Bilthoven/908/1969 1969. -15.5432 -2.4709 na 17 | virus A/Bilthoven/17938/1969 1969. -14.1924 -3.135 na 18 | virus A/Bilthoven/93/1970 1970. -15.5105 -2.8699 na 19 | virus A/Bilthoven/2668/1970 1970. -15.3049 -6.1481 na 20 | virus A/Bilthoven/6449/1971 1971. -14.4675 -5.9153 na 21 | virus A/Bilthoven/21438/1971 1971. -13.6731 -4.0881 na 22 | virus A/Bilthoven/21801/1971 1971. -14.5943 -3.5782 na 23 | virus A/HongKong/107/1971 1971. -12.9848 -5.8648 na 24 | virus A/Bilthoven/6022/1972 1972. -13.8737 -3.1447 na 25 | virus A/Bilthoven/21793/1972 1972. -11.5254 -4.3371 na 26 | virus A/Bilthoven/23290/1972 1972. -11.9895 -3.7082 na 27 | virus A/Bilthoven/23337/1972 1972. -11.5635 -4.4806 na 28 | virus A/England/42/1972 1972. -10.6403 -4.2246 na 29 | virus A/Bilthoven/552/1973 1973. -10.5876 -3.5934 na 30 | virus A/Bilthoven/748/1973 1973. -13.2184 -2.8953 na 31 | virus A/Bilthoven/3517/1973 1973. -12.5122 -3.9598 na 32 | virus A/PortChalmers/1/1973 1973. -9.0882 -4.007 na 33 | virus A/Bilthoven/5146/1974 1974. -11.1024 -5.5403 na 34 | virus A/Bilthoven/5930/1974 1974. -11.1957 -5.0042 na 35 | virus A/Bilthoven/5931/1974 1974. -10.5149 -4.8432 na 36 | virus A/Bilthoven/7398/1974 1974. -9.9636 -4.6786 na 37 | virus A/Bilthoven/9459/1974 1974. -10.8702 -3.6208 na 38 | virus A/Bilthoven/4273/1975 1975. -10.3227 -6.328 na 39 | virus A/Bilthoven/334/1975 1975. -9.7907 -5.1856 na 40 | virus A/Bilthoven/1843/1975 1975. -10.4165 -2.9183 na 41 | virus A/Bilthoven/2600/1975 1975. -11.7597 -5.5978 na 42 | virus A/Bilthoven/2813/1975 1975. -11.5391 -4.8783 na 43 | virus A/Victoria/3/1975 1975. -8.4946 -1.8687 na 44 | virus A/Bilthoven/5168/1976 1976. -6.9522 -1.0372 na 45 | virus A/Bilthoven/628/1976 1976. -7.1951 1.1066 na 46 | virus A/Bilthoven/1761/1976 1976. -8.1943 -0.3938 na 47 | virus A/Bilthoven/2271/1976 1976. -7.1647 1.6784 na 48 | virus A/Bilthoven/5029/1976 1976. -7.1206 -1.6353 na 49 | virus A/Bilthoven/5657/1976 1976. -6.9841 -1.1677 na 50 | virus A/Bilthoven/6545/1976 1976. -7.6214 -1.4829 na 51 | virus A/Amsterdam/1609/1977 1977. -8.3539 -0.55 na 52 | virus A/Bilthoven/3895/1977 1977. -7.8375 -1.3772 na 53 | virus A/Rotterdam/5828/1977 1977. -8.849 -1.9919 na 54 | virus A/Rotterdam/8179/1977 1977. -8.0522 -1.0929 na 55 | virus A/Texas/1/1977 1977. -8.2743 2.7299 na 56 | virus A/Bangkok/1/1979 1979. -7.09 6.9542 na 57 | virus A/Netherlands/209/1980 1980. -7.177 3.7985 na 58 | virus A/Lyon/2380/1981 1981. -6.0039 4.719 na 59 | virus A/Bilthoven/4791/1981 1981. -6.1393 3.5288 na 60 | virus A/Netherlands/233/1982 1982. -6.648 4.0834 na 61 | virus A/Netherlands/241/1982 1982. -7.09 3.7396 na 62 | virus A/Bilthoven/10684/1982 1982. -6.3841 2.9527 na 63 | virus A/Philippines/2/1982 1982. -6.1311 6.2222 na 64 | virus A/Oslow/13676/1983 1983. -7.0839 3.9902 na 65 | virus A/Caen/1/1984 1984. -5.9562 2.3071 na 66 | virus A/Netherlands/330/1985 1985. -5.1828 3.6016 na 67 | virus A/Stockholm/10/1985 1985. -5.0263 3.7497 na 68 | virus A/Wellington/4/1985 1985. -4.6627 3.6501 na 69 | virus A/Netherlands/333/1985 1985. -5.8433 2.0197 na 70 | virus A/Guildford/V728/1985 1985. -2.7192 5.4545 na 71 | virus A/Colorado/2/1986 1986. -5.0849 3.971 na 72 | virus A/Leningrad/360/1986 1986. -4.7285 6.7329 na 73 | virus A/Sichuan/2/1987 1987. -2.9534 6.4264 na 74 | virus A/Victoria/7/1987 1987. -2.8321 1.3547 na 75 | virus A/Shanghai/11/1987 1987. -1.5178 6.7235 na 76 | virus A/Netherlands/450/1988 1988. -1.1515 3.4974 na 77 | virus A/Victoria/1/1988 1988. -2.8627 0.9763 na 78 | virus A/Stockholm/12/1988 1988. -1.7925 3.2882 na 79 | virus A/England/427/1988 1988. -0.5554 3.6901 na 80 | virus A/Netherlands/620/1989 1989. -0.6045 3.1085 na 81 | virus A/England//1989 1989. -1.9394 4.1911 na 82 | virus A/Geneva/5007/1989 1989. -1.2235 3.0939 na 83 | virus A/Guizhou/54/1989 1989. -1.3026 6.0351 na 84 | virus A/HongKong/1/1989 1989. -1.1622 4.0588 na 85 | virus A/Netherlands/650/1989 1989. 0.3095 4.1192 na 86 | virus A/Netherlands/738/1989 1989. -0.0119 6.1672 na 87 | virus A/Singapore/35/1989 1989. -0.006 4.3364 na 88 | virus A/Singapore/40/1989 1989. -1.7896 1.5092 na 89 | virus A/Wellington/5/1989 1989. -1.8942 6.4989 na 90 | virus A/Beijing/353/1989 1989. -1.7072 -1.2335 na 91 | virus A/Beijing/352/1989 1989. 1.1535 0.2009 na 92 | virus A/Atlanta/211/1989 1989. -1.9754 2.59 na 93 | virus A/Singapore/34/1989 1989. 0.492 3.8876 na 94 | virus A/Singapore/36/1989 1989. -0.3443 2.3136 na 95 | virus A/Singapore/53/1989 1989. 0.1146 4.0298 na 96 | virus A/Victoria/1/1989 1989. -1.1223 7.3679 na 97 | virus A/Victoria/2/1990 1990. 0.105 0.248 na 98 | virus A/Wellington/3/1990 1990. 0.1347 0.7354 na 99 | virus A/Memphis/2/1990 1990. -1.485 4.5472 na 100 | virus A/Seoul/1/1990 1990. -0.9797 3.4092 na 101 | virus A/Memphis/5/1990 1990. -1.811 2.4699 na 102 | virus A/Shanghai/24/1990 1990. 2.6657 5.087 na 103 | virus A/Lyon/1149/1991 1991. 1.0081 -0.7483 na 104 | virus A/Netherlands/891/1991 1991. -1.448 0.6257 na 105 | virus A/Canberra/1/1991 1991. -1.8131 3.0883 na 106 | virus A/England/260/1991 1991. -0.7894 -0.1566 na 107 | virus A/England/261/1991 1991. 1.3419 -0.0771 na 108 | virus A/Madrid/G12/1991 1991. -1.231 -0.5099 na 109 | virus A/Netherlands/816/1991 1991. -0.9219 -1.3274 na 110 | virus A/Geneva/5366/1991 1991. -0.391 3.5758 na 111 | virus A/Lyon/1182/1991 1991. 0.6691 -0.7697 na 112 | virus A/Geneva/6447/1991 1991. -1.2843 -1.5868 na 113 | virus A/Lyon/1189/1991 1991. -0.3627 -0.088 na 114 | virus A/Lyon/1276/1991 1991. 1.2934 -0.9213 na 115 | virus A/Lyon/1337/1991 1991. 2.0586 0.1288 na 116 | virus A/Lyon/1373/1991 1991. 0.5379 -1.1161 na 117 | virus A/Lyon/1594/1991 1991. -0.7665 -1.3646 na 118 | virus A/Lyon/23672/1991 1991. -0.8155 -1.6754 na 119 | virus A/Lyon/24103/1991 1991. -1.1945 -0.6845 na 120 | virus A/Lyon/24222/1991 1991. 2.1927 1.0413 na 121 | virus A/Stockholm/20/1991 1991. -0.5177 -0.8534 na 122 | virus A/Victoria/33/1992 1992. -0.0418 0.5078 na 123 | virus A/Amsterdam/4112/1992 1992. 0.2483 0.4378 na 124 | virus A/Enschede/1285/1992 1992. -0.2424 -0.5747 na 125 | virus A/Finland/220/1992 1992. 0.9153 -1.4369 na 126 | virus A/Madrid/G58/1992 1992. 0.9735 -0.67 na 127 | virus A/Nijmegen/3129/1992 1992. -0.3922 -1.0866 na 128 | virus A/Netherlands/819/1992 1992. 0.3728 0.0191 na 129 | virus A/Netherlands/935/1992 1992. -0.3247 0.5154 na 130 | virus A/Paris/583/1992 1992. -1.3787 -0.9108 na 131 | virus A/Paris/614/1992 1992. -0.6399 -0.6478 na 132 | virus A/SouthAustralia/8/1992 1992. -1.0842 -2.0371 na 133 | virus A/SouthAustralia/23/1992 1992. -1.6336 -0.8624 na 134 | virus A/SouthAustralia/27/1992 1992. -0.1539 -1.9155 na 135 | virus A/Stockholm/7/1992 1992. -2.1563 -0.7443 na 136 | virus A/Victoria/68/1992 1992. -1.0016 0.106 na 137 | virus A/Paris/467/1992 1992. -1.8534 0.4993 na 138 | virus A/Tilburg/5957/1992 1992. -0.2765 0.0863 na 139 | virus A/Beijing/32/1992 1992. 4.1541 4.9999 na 140 | virus A/Finland/247/1992 1992. 6.5173 4.2346 na 141 | virus A/Netherlands/938/1992 1992. 3.4144 4.7316 na 142 | virus A/Sendai/C273/1992 1992. 6.9405 5.7598 na 143 | virus A/Stockholm/12/1992 1992. 5.3167 2.4805 na 144 | virus A/Stockholm/13/1992 1992. -1.076 -0.4021 na 145 | virus A/Umea/1982/1992 1992. 2.1923 -0.0314 na 146 | virus A/Umea/2000/1992 1992. 0.1544 -1.1116 na 147 | virus A/Finland/218/1992 1992. -0.4116 -2.1285 na 148 | virus A/Geneva/5113/1992 1992. -2.4748 -1.0317 na 149 | virus A/Houston/56798/1992 1992. -0.7595 -1.972 na 150 | virus A/Houston/56829/1992 1992. -0.1597 -0.0519 na 151 | virus A/Houston/56941/1992 1992. 0.5469 -0.1815 na 152 | virus A/Nijmegen/3126/1992 1992. -0.4322 -0.9956 na 153 | virus A/Netherlands/823/1992 1992. 0.1183 -0.4592 na 154 | virus A/Paris/320/1992 1992. -0.6873 -0.5864 na 155 | virus A/Paris/325/1992 1992. -0.2705 -0.7563 na 156 | virus A/Paris/407/1992 1992. -1.5648 -1.2151 na 157 | virus A/Paris/417/1992 1992. 0.7011 -1.1943 na 158 | virus A/Paris/424/1992 1992. -0.0636 -1.3489 na 159 | virus A/Paris/457/1992 1992. -1.6433 -1.349 na 160 | virus A/Paris/490/1992 1992. 0.0704 -0.9108 na 161 | virus A/Paris/512/1992 1992. -0.9947 -1.5049 na 162 | virus A/Paris/548/1992 1992. -1.6222 -1.275 na 163 | virus A/Paris/564/1992 1992. 0.9902 -0.929 na 164 | virus A/Paris/597/1992 1992. 0.2007 -1.7357 na 165 | virus A/Rotterdam/100540/1992 1992. -0.6154 -0.6254 na 166 | virus A/Stockholm/8/1992 1992. 0.3531 -1.7533 na 167 | virus A/Madrid/G102/1993 1993. 5.4589 1.959 na 168 | virus A/Madrid/G252/1993 1993. 6.343 -1.7372 na 169 | virus A/Akita/4/1993 1993. 7.1333 4.1097 na 170 | virus A/Enschede/5458/1993 1993. 2.0721 -1.0684 na 171 | virus A/Madrid/G101/1993 1993. -0.6204 -0.5268 na 172 | virus A/Madrid/G109/1993 1993. 5.9952 2.4166 na 173 | virus A/Madrid/G116/1993 1993. -0.4595 -1.1112 na 174 | virus A/Madrid/G122/1993 1993. 7.1676 1.5127 na 175 | virus A/Madrid/G130/1993 1993. 5.4686 4.6347 na 176 | virus A/Netherlands/3/1993 1993. 4.3285 2.1466 na 177 | virus A/Netherlands/17/1993 1993. 3.6902 3.9175 na 178 | virus A/Netherlands/101/1993 1993. 4.8405 5.4876 na 179 | virus A/Netherlands/115/1993 1993. 4.4623 4.9382 na 180 | virus A/Netherlands/126/1993 1993. 4.5739 4.7341 na 181 | virus A/Netherlands/165/1993 1993. -0.8839 -2.2992 na 182 | virus A/Netherlands/179/1993 1993. 4.1154 3.5142 na 183 | virus A/Paris/287/1993 1993. -0.2916 -0.9913 na 184 | virus A/Shiga/6/1993 1993. 6.5967 4.4533 na 185 | virus A/Yamagata/56/1993 1993. 7.1968 4.4855 na 186 | virus A/Yamagata/61/1993 1993. 7.4635 6.1592 na 187 | virus A/Yamagata/62/1993 1993. 7.5563 5.0138 na 188 | virus A/Netherlands/399/1993 1993. 5.4567 -1.3313 na 189 | virus A/Shangdong/9/1993 1993. 6.6098 4.5581 na 190 | virus A/Lyon/672/1993 1993. 5.8004 3.556 na 191 | virus A/Lyon/1803/1993 1993. 5.8696 2.5392 na 192 | virus A/Netherlands/357/1993 1993. 5.4036 2.3464 na 193 | virus A/Netherlands/371/1993 1993. 7.929 3.1416 na 194 | virus A/Netherlands/372/1993 1993. 5.1431 -1.6674 na 195 | virus A/Netherlands/398/1993 1993. 6.0659 1.9889 na 196 | virus A/Netherlands/440/1993 1993. 4.6648 2.6902 na 197 | virus A/Oslow/2219/1993 1993. 7.0941 1.3277 na 198 | virus A/Oslow/2352/1993 1993. 6.6233 4.5603 na 199 | virus A/Stockholm/20/1993 1993. 5.6879 1.211 na 200 | virus A/Victoria/104/1993 1993. 6.1619 3.6055 na 201 | virus A/Wellington/59/1993 1993. 7.0425 3.864 na 202 | virus A/Singapore/19/1993 1993. 6.0906 -1.0217 na 203 | virus A/Lyon/1815/1993 1993. 7.0821 1.6206 na 204 | virus A/Lyon/22686/1993 1993. 6.3967 3.3353 na 205 | virus A/Lyon/23602/1993 1993. 5.4155 0.9162 na 206 | virus A/Singapore/3/1993 1993. 4.9307 4.0125 na 207 | virus A/Guangdong/25/1993 1993. 7.4392 3.0542 na 208 | virus A/Scotland/142/1993 1993. 5.5846 3.5379 na 209 | virus A/Scotland/160/1993 1993. 7.207 3.745 na 210 | virus A/HongKong/1/1994 1994. 6.4428 1.5648 na 211 | virus A/HongKong/2/1994 1994. 4.6175 -0.9359 na 212 | virus A/HongKong/56/1994 1994. 6.4251 1.7921 na 213 | virus A/SouthAustralia/15/1994 1994. 6.239 1.1308 na 214 | virus A/SouthAustralia/25/1994 1994. 7.0066 1.6433 na 215 | virus A/Netherlands/18/1994 1994. 6.1312 1.5459 na 216 | virus A/Finland/338/1995 1995. 5.5091 -1.2183 na 217 | virus A/Stockholm/506/1995 1995. 6.0812 0.2756 na 218 | virus A/Geneva/AI9509/1995 1995. 4.8626 -0.8163 na 219 | virus A/Finland/339/1995 1995. 10.0174 -1.2134 na 220 | virus A/HongKong/3/1995 1995. 6.3768 2.9917 na 221 | virus A/Finland/381/1995 1995. 8.5653 -1.422 na 222 | virus A/HongKong/38/1995 1995. 5.7564 1.9729 na 223 | virus A/HongKong/49/1995 1995. 7.0938 -0.4838 na 224 | virus A/HongKong/55/1995 1995. 5.2927 -0.8529 na 225 | virus A/Lyon/2279/1995 1995. 6.046 -0.1329 na 226 | virus A/Nanchang/933/1995 1995. 5.3121 -0.7875 na 227 | virus A/Netherlands/271/1995 1995. 7.4855 -2.9466 na 228 | virus A/Victoria/75/1995 1995. 6.0681 1.265 na 229 | virus A/Wuhan/359/1995 1995. 4.7321 -0.962 na 230 | virus A/Brisbane/8/1996 1996. 4.2296 -3.3188 na 231 | virus A/Geneva/3958/1996 1996. 5.7644 -1.6062 na 232 | virus A/HongKong/20/1996 1996. 5.4143 -2.0893 na 233 | virus A/HongKong/42/1996 1996. 6.7466 2.2872 na 234 | virus A/HongKong/357/1996 1996. 5.9514 -1.8157 na 235 | virus A/HongKong/358/1996 1996. 4.6812 -2.6652 na 236 | virus A/HongKong/434/1996 1996. 9.3424 3.4865 na 237 | virus A/Netherlands/91/1996 1996. 6.1304 3.4925 na 238 | virus A/Singapore/1/1996 1996. 4.6392 -1.8924 na 239 | virus A/Lyon/1781/1996 1996. 5.248 -1.5335 na 240 | virus A/HongKong/1/1997 1997. 4.8948 -2.0298 na 241 | virus A/Nice/491/1997 1997. 5.1986 -2.869 na 242 | virus A/Auckland/10/1997 1997. 5.6159 -6.5705 na 243 | virus A/HongKong/280/1997 1997. 4.2037 -2.7282 na 244 | virus A/Netherlands/300/1997 1997. 7.0705 -6.5258 na 245 | virus A/Sydney/5/1997 1997. 5.8935 -6.5485 na 246 | virus A/Johannesburg/10/1997 1997. 5.1199 -2.2143 na 247 | virus A/Oslow/21/1997 1997. 4.877 -1.3639 na 248 | virus A/Oslow/244/1997 1997. 5.106 -2.2767 na 249 | virus A/Netherlands/5/1998 1998. 4.8839 -1.2065 na 250 | virus A/Netherlands/414/1998 1998. 6.1827 -4.9517 na 251 | virus A/Netherlands/462/1998 1998. 5.9292 -4.7947 na 252 | virus A/Netherlands/427/1998 1998. 5.492 -6.1908 na 253 | virus A/Moscow/10/1999 1999. 4.4339 -6.692 na 254 | virus A/Netherlands/301/1999 1999. 6.2833 -6.4353 na 255 | virus A/Panama/2007/1999 1999. 6.1231 -6.2043 na 256 | virus A/Netherlands/3/2000 2000. 9.2532 -5.7247 na 257 | virus A/Netherlands/118/2001 2001. 6.4392 -7.0799 na 258 | virus A/Netherlands/126/2001 2001. 7.0916 -4.905 na 259 | virus A/Netherlands/124/2001 2001. 8.1868 -4.916 na 260 | virus A/Netherlands/1/2002 2002. 9.5442 -4.9321 na 261 | virus A/Netherlands/120/2002 2002. 6.1867 -6.0198 na 262 | virus A/Fujian/411/2002 2002. 9.151 -10.0664 na 263 | virus A/Netherlands/22/2003 2003. 10.9371 -6.9132 na 264 | virus A/Netherlands/213/2003 2003. 8.4727 -7.3674 na 265 | virus A/Netherlands/217/2003 2003. 8.6558 -8.9489 na 266 | virus A/Netherlands/222/2003 2003. 9.6596 -7.3881 na 267 | virus A/Finland/170/2003 2003. 8.5957 -8.1251 na 268 | virus A/Netherlands/20/2003 2003. 7.5101 -5.4674 na 269 | virus AL/4382/82 1982. -6.9387 5.0332 na 270 | virus OK/5/88 1988. -3.5523 -0.4674 na 271 | virus AT/3572DASH5/88 1988. -1.9119 3.5837 na 272 | virus EI/3447/89 1989. -1.1691 2.6446 na 273 | virus WK/1/89 1989. -0.8788 3.8758 na 274 | virus OV/31/92 1992. -0.3947 0.6488 na 275 | serum CC/4/85 1985. -6.84 4.3768 10.1293 276 | serum NL/330/85 1985. -4.626 4.0674 11.3219 277 | serum NL/450/88 1988. -2.0232 3.5509 13.3219 278 | serum WE/4/85 1985. -3.4214 3.4418 12.3219 279 | serum PR/413/94 1994. 6.5211 0.7183 11.3219 280 | serum TE/1A/77 1977. -8.3457 2.0656 10.9887 281 | serum PH/2/82 1982. -8.2772 5.3889 12.3219 282 | serum VI/7/87 1987. -1.6981 2.3167 11.3219 283 | serum SI/2/87 1987. -1.827 4.4707 11.9887 284 | serum EN/496/80 1980. -7.9445 5.2337 12.3219 285 | serum HK/1/68 1968. -15.2301 -3.4003 10.3219 286 | serum EN/42/72 1972. -12.3396 -1.9789 12.3219 287 | serum PC/1/73 1973. -10.6669 -2.9924 11.3219 288 | serum VI/3A/75 1975. -9.5283 -0.8823 11.3219 289 | serum LE/360/86 1986. -4.9851 2.9435 11.3219 290 | serum BA/1/79 1979. -7.3931 6.0349 10.3219 291 | serum SL/840/74 1974. -9.0371 -5.3351 11.3219 292 | serum BI/21793/72 1972. -12.6477 -3.683 10.3219 293 | serum BI/5930/74 1974. -10.1877 -2.8768 10.3219 294 | serum AM/1609/77 1977. -7.45 0.3157 11.3219 295 | serum BI/2461/78 1978. -7.9704 4.2827 11.8218 296 | serum RD/577/80 1980. -8.7711 6.3967 12.3219 297 | serum NL/209/80 1980. -9.5186 4.0463 12.3219 298 | serum NL/233/82 1982. -7.9755 4.1804 11.3219 299 | serum NL/241/82 1982. -8.0868 4.4245 12.3219 300 | serum ST/10/85 1985. -4.4502 2.7682 11.8218 301 | serum VI/2/90 1990. -0.6135 0.5062 12.3219 302 | serum LY/1149/91 1991. 0.6597 -0.1424 11.3219 303 | serum MA/G252/93 1993. 6.5494 0.73 10.0715 304 | serum NL/1/95 1995. 8.2038 2.08 12.3219 305 | serum NL/218/95 1995. 8.2414 0.9078 11.7065 306 | serum NL/172/96 1996. 6.9508 -1.4166 11.3219 307 | serum TE/1B/77 1977. -8.6953 2.7945 13.3219 308 | serum BA/2/79 1979. -6.1259 4.016 11.3219 309 | serum CE/1B/84 1984. -5.4713 2.9279 9.3219 310 | serum CO/2/86 1986. -3.5769 2.6624 13.3219 311 | serum BE/353/89 1989. 0.5472 1.1582 12.3219 312 | serum VI/3C/75 1975. -7.9412 -0.243 11.3219 313 | serum SH/11/87 1987. -1.3682 5.0625 13.3219 314 | serum GD/25/93 1993. 9.2242 1.4192 12.9069 315 | serum JO/33/94 1994. 8.7544 1.7819 12.9069 316 | serum NL/47/95 1995. 7.1448 0.0913 10.9069 317 | serum NA/933/95 1995. 7.5272 -2.1656 10.3219 318 | serum LY/2279/95 1995. 8.3346 -0.5602 12.1293 319 | serum SP/1/96 1996. 3.4224 -1.0379 11.5718 320 | serum AU/10/97 1997. 6.1995 -5.1109 12.1144 321 | serum NL/5/98 1998. 7.6363 -1.8004 12.3219 322 | serum NL/18/94 1994. 8.0076 -1.5475 11.9069 323 | serum HK/107/71 1971. -16.0617 -6.06 12.3219 324 | serum PH/2V/82 1982. -8.2119 5.5705 11.2761 325 | serum BE/32V/92 1992. 3.0406 4.2812 10.0941 326 | serum NL/286/97 1997. 5.3936 -2.0472 9.9069 327 | serum SY/5V/97 1997. 5.9086 -7.472 12.9069 328 | serum GU/54/89 1989. -0.1843 3.8468 13.3219 329 | serum NL/333/85 1985. -5.5564 3.9095 10.3219 330 | serum CE/1A/84 1984. -5.5184 3.7426 10.3219 331 | serum SH/31/80 1980. -6.5479 3.2165 9.9069 332 | serum NL/620/89 1989. -0.7659 2.6776 14.3219 333 | serum BE/32A/92 1992. 4.9572 2.3595 10.4828 334 | serum HK/34/90 1990. 1.6771 3.8046 13.3219 335 | serum BE/32B/92 1992. 4.3194 3.4286 9.8218 336 | serum FI/338/95 1995. 7.9808 1.2118 13.3219 337 | serum SD/9/93 1993. 5.8466 2.0457 12.1293 338 | serum OS/2352/93 1993. 6.2611 2.2469 10.8796 339 | serum GE/A9509/95 1995. 6.6473 0.9578 11.4681 340 | serum BR/8/96 1996. 6.3455 -1.8503 11.5718 341 | serum SY/5B/97 1997. 7.3383 -5.9596 12.9069 342 | serum SY/5A/97 1997. 5.6227 -5.4229 11.9894 343 | serum WU/359B/95 1995. 5.3271 -1.7993 11.3219 344 | serum MW/10/99 1999. 6.7862 -6.655 11.7752 345 | serum SY/5HAY/97 1997. 7.9597 -6.3657 11.9069 346 | serum NL/1/02 2002. 6.9499 -5.9009 11.3219 347 | serum PM/2007/99 1999. 6.2532 -7.0724 11.7258 348 | serum NL/126/01 2001. 6.7494 -5.9118 11.3219 349 | serum NL/118/01 2001. 6.2008 -5.8021 11.5182 350 | serum FU/411/02 2002. 10.5715 -8.901 12.9885 351 | serum NL/88/03 2003. 7.1686 -6.6281 11.9069 352 | serum NL/22/03 2003. 9.3644 -8.1153 12.5365 353 | serum NL/124/01 2001. 6.34 -7.1 11.9069 -------------------------------------------------------------------------------- /figure-data/fig11_smith_mds_drift.tsv: -------------------------------------------------------------------------------- 1 | type name year ag1 ag2 potency 2 | virus A/Rotterdam/577/1980 1980. -7.3672 1.5776 na 3 | virus A/ChristChurch/2/1988 1988. -4.9305 -0.7725 na 4 | virus A/Netherlands/241/1993 1993. 5.3776 2.4348 na 5 | virus A/HongKong/55/1994 1994. 5.8437 0.895 na 6 | virus A/England/7/1994 1994. 7.7639 -0.9509 na 7 | virus A/Johannesburg/33/1994 1994. 5.9543 4.5837 na 8 | virus A/Johannesburg/47/1994 1994. 4.6162 4.2461 na 9 | virus A/Netherlands/1/1995 1995. 7.0362 2.9031 na 10 | virus A/HongKong/32/1995 1995. 5.6777 1.4108 na 11 | virus A/Bilthoven/15793/1968 1968. -18.2935 -1.457 na 12 | virus A/Bilthoven/16190/1968 1968. -17.6771 -0.4413 na 13 | virus A/Bilthoven/16398/1968 1968. -17.275 -2.4468 na 14 | virus A/HongKong/1/1968 1968. -18.6493 -2.3933 na 15 | virus A/Bilthoven/808/1969 1969. -17.2701 -0.6887 na 16 | virus A/Bilthoven/908/1969 1969. -17.6359 -1.3156 na 17 | virus A/Bilthoven/17938/1969 1969. -18.1398 -1.3908 na 18 | virus A/Bilthoven/93/1970 1970. -17.5245 -1.2836 na 19 | virus A/Bilthoven/2668/1970 1970. -18.4311 -1.0237 na 20 | virus A/Bilthoven/6449/1971 1971. -18.734 0.1097 na 21 | virus A/Bilthoven/21438/1971 1971. -16.9978 -2.2221 na 22 | virus A/Bilthoven/21801/1971 1971. -17.2659 -0.2418 na 23 | virus A/HongKong/107/1971 1971. -18.2994 -1.0332 na 24 | virus A/Bilthoven/6022/1972 1972. -16.2207 -0.8929 na 25 | virus A/Bilthoven/21793/1972 1972. -15.7677 -0.1073 na 26 | virus A/Bilthoven/23290/1972 1972. -15.6242 0.9815 na 27 | virus A/Bilthoven/23337/1972 1972. -15.1723 -0.4141 na 28 | virus A/England/42/1972 1972. -14.9293 -2.6824 na 29 | virus A/Bilthoven/552/1973 1973. -13.5471 -0.9215 na 30 | virus A/Bilthoven/748/1973 1973. -15.3344 0.6018 na 31 | virus A/Bilthoven/3517/1973 1973. -15.6834 -1.1155 na 32 | virus A/PortChalmers/1/1973 1973. -12.1679 -2.9291 na 33 | virus A/Bilthoven/5146/1974 1974. -14.7603 0.6033 na 34 | virus A/Bilthoven/5930/1974 1974. -15.548 -1.0226 na 35 | virus A/Bilthoven/5931/1974 1974. -15.5273 1.4548 na 36 | virus A/Bilthoven/7398/1974 1974. -14.9708 0.2102 na 37 | virus A/Bilthoven/9459/1974 1974. -14.4008 -0.52 na 38 | virus A/Bilthoven/4273/1975 1975. -13.9122 -2.7946 na 39 | virus A/Bilthoven/334/1975 1975. -14.8895 0.8009 na 40 | virus A/Bilthoven/1843/1975 1975. -14.2026 1.0313 na 41 | virus A/Bilthoven/2600/1975 1975. -13.9228 -2.8886 na 42 | virus A/Bilthoven/2813/1975 1975. -15.5407 1.3689 na 43 | virus A/Victoria/3/1975 1975. -10.7179 -1.9859 na 44 | virus A/Bilthoven/5168/1976 1976. -11.9334 0.7019 na 45 | virus A/Bilthoven/628/1976 1976. -8.8289 0.4538 na 46 | virus A/Bilthoven/1761/1976 1976. -9.9193 -1.698 na 47 | virus A/Bilthoven/2271/1976 1976. -8.2471 0.1642 na 48 | virus A/Bilthoven/5029/1976 1976. -9.7991 -2.346 na 49 | virus A/Bilthoven/5657/1976 1976. -9.7314 -2.1303 na 50 | virus A/Bilthoven/6545/1976 1976. -9.38 -1.3624 na 51 | virus A/Amsterdam/1609/1977 1977. -10.2321 -1.8492 na 52 | virus A/Bilthoven/3895/1977 1977. -9.8469 -1.9507 na 53 | virus A/Rotterdam/5828/1977 1977. -11.4347 -2.4532 na 54 | virus A/Rotterdam/8179/1977 1977. -10.5228 -1.715 na 55 | virus A/Texas/1/1977 1977. -9.8808 2.0822 na 56 | virus A/Bangkok/1/1979 1979. -7.2906 4.4582 na 57 | virus A/Netherlands/209/1980 1980. -7.1903 1.8027 na 58 | virus A/Lyon/2380/1981 1981. -6.033 3.4034 na 59 | virus A/Bilthoven/4791/1981 1981. -7.4718 1.2729 na 60 | virus A/Netherlands/233/1982 1982. -7.1262 1.1887 na 61 | virus A/Netherlands/241/1982 1982. -6.7209 2.0468 na 62 | virus A/Bilthoven/10684/1982 1982. -6.7741 1.961 na 63 | virus A/Philippines/2/1982 1982. -6.9382 4.6132 na 64 | virus A/Oslow/13676/1983 1983. -6.1473 2.9082 na 65 | virus A/Caen/1/1984 1984. -6.2118 0.3594 na 66 | virus A/Netherlands/330/1985 1985. -6.1111 0.3727 na 67 | virus A/Stockholm/10/1985 1985. -5.0213 0.892 na 68 | virus A/Wellington/4/1985 1985. -4.738 0.5498 na 69 | virus A/Netherlands/333/1985 1985. -3.9823 1.4445 na 70 | virus A/Guildford/V728/1985 1985. -5.0876 -0.6705 na 71 | virus A/Colorado/2/1986 1986. -5.3536 0.7596 na 72 | virus A/Leningrad/360/1986 1986. -3.2942 4.0323 na 73 | virus A/Sichuan/2/1987 1987. -2.7864 3.9083 na 74 | virus A/Victoria/7/1987 1987. -4.0667 -2.5606 na 75 | virus A/Shanghai/11/1987 1987. -1.0898 2.3186 na 76 | virus A/Netherlands/450/1988 1988. -2.5708 -0.4461 na 77 | virus A/Victoria/1/1988 1988. -4.7806 -1.4152 na 78 | virus A/Stockholm/12/1988 1988. -2.444 -0.067 na 79 | virus A/England/427/1988 1988. -3.4675 2.2412 na 80 | virus A/Netherlands/620/1989 1989. -1.359 0.0597 na 81 | virus A/England//1989 1989. -1.5492 1.2869 na 82 | virus A/Geneva/5007/1989 1989. -2.1444 0.7973 na 83 | virus A/Guizhou/54/1989 1989. -0.4618 2.7335 na 84 | virus A/HongKong/1/1989 1989. -1.8117 0.8551 na 85 | virus A/Netherlands/650/1989 1989. -1.3092 1.4828 na 86 | virus A/Netherlands/738/1989 1989. -0.5634 2.4095 na 87 | virus A/Singapore/35/1989 1989. -0.9521 1.8049 na 88 | virus A/Singapore/40/1989 1989. -0.4388 0.9774 na 89 | virus A/Wellington/5/1989 1989. -0.3377 1.0067 na 90 | virus A/Beijing/353/1989 1989. -0.85 4.1106 na 91 | virus A/Beijing/352/1989 1989. 1.5603 -1.472 na 92 | virus A/Atlanta/211/1989 1989. -1.3296 -0.3599 na 93 | virus A/Singapore/34/1989 1989. -0.9965 1.3942 na 94 | virus A/Singapore/36/1989 1989. 0.3847 -0.2927 na 95 | virus A/Singapore/53/1989 1989. -1.5583 -0.2436 na 96 | virus A/Victoria/1/1989 1989. -3.5183 4.2805 na 97 | virus A/Victoria/2/1990 1990. 0.403 -2.0271 na 98 | virus A/Wellington/3/1990 1990. 0.7149 -2.5168 na 99 | virus A/Memphis/2/1990 1990. -2.7198 0.4416 na 100 | virus A/Seoul/1/1990 1990. -2.385 1.0147 na 101 | virus A/Memphis/5/1990 1990. -1.4629 -0.6008 na 102 | virus A/Shanghai/24/1990 1990. 0.5911 4.1553 na 103 | virus A/Lyon/1149/1991 1991. 1.4147 -2.6217 na 104 | virus A/Netherlands/891/1991 1991. 0.3923 -2.7945 na 105 | virus A/Canberra/1/1991 1991. -1.6219 0.4801 na 106 | virus A/England/260/1991 1991. 0.2705 -2.4828 na 107 | virus A/England/261/1991 1991. 2.39 0.2479 na 108 | virus A/Madrid/G12/1991 1991. -0.1318 -2.7039 na 109 | virus A/Netherlands/816/1991 1991. -0.0945 -2.5952 na 110 | virus A/Geneva/5366/1991 1991. -1.6403 1.5454 na 111 | virus A/Lyon/1182/1991 1991. 1.6654 -1.8241 na 112 | virus A/Geneva/6447/1991 1991. 0.6606 -3.1415 na 113 | virus A/Lyon/1189/1991 1991. 1.0765 -0.9727 na 114 | virus A/Lyon/1276/1991 1991. 2.2584 -1.4946 na 115 | virus A/Lyon/1337/1991 1991. 1.7465 -2.3886 na 116 | virus A/Lyon/1373/1991 1991. 1.1729 -2.0984 na 117 | virus A/Lyon/1594/1991 1991. -0.0139 -2.8783 na 118 | virus A/Lyon/23672/1991 1991. 0.8845 -2.9212 na 119 | virus A/Lyon/24103/1991 1991. 0.5167 -2.271 na 120 | virus A/Lyon/24222/1991 1991. 1.1032 -1.199 na 121 | virus A/Stockholm/20/1991 1991. -0.0896 -3.046 na 122 | virus A/Victoria/33/1992 1992. 0.5778 -1.448 na 123 | virus A/Amsterdam/4112/1992 1992. 0.4078 -2.0973 na 124 | virus A/Enschede/1285/1992 1992. -0.3705 -3.0753 na 125 | virus A/Finland/220/1992 1992. 1.542 -2.7233 na 126 | virus A/Madrid/G58/1992 1992. 0.7866 -1.6093 na 127 | virus A/Nijmegen/3129/1992 1992. 0.1412 -1.7276 na 128 | virus A/Netherlands/819/1992 1992. 1.1743 -1.4375 na 129 | virus A/Netherlands/935/1992 1992. 0.1075 -1.2427 na 130 | virus A/Paris/583/1992 1992. -0.2161 -4.0064 na 131 | virus A/Paris/614/1992 1992. 0.6015 -2.1298 na 132 | virus A/SouthAustralia/8/1992 1992. 1.1746 -4.3357 na 133 | virus A/SouthAustralia/23/1992 1992. -0.4457 -3.7943 na 134 | virus A/SouthAustralia/27/1992 1992. 2.3358 -3.4244 na 135 | virus A/Stockholm/7/1992 1992. -1.4649 -3.1956 na 136 | virus A/Victoria/68/1992 1992. 0.631 0.006 na 137 | virus A/Paris/467/1992 1992. -0.578 -2.1269 na 138 | virus A/Tilburg/5957/1992 1992. 0.6028 -2.5945 na 139 | virus A/Beijing/32/1992 1992. 2.9106 4.2419 na 140 | virus A/Finland/247/1992 1992. 4.4759 4.2999 na 141 | virus A/Netherlands/938/1992 1992. 1.6655 3.5259 na 142 | virus A/Sendai/C273/1992 1992. 4.4985 5.4887 na 143 | virus A/Stockholm/12/1992 1992. 3.8876 3.8684 na 144 | virus A/Stockholm/13/1992 1992. 0.2179 -1.6496 na 145 | virus A/Umea/1982/1992 1992. 1.4455 -3.1433 na 146 | virus A/Umea/2000/1992 1992. 0.7221 -2.3967 na 147 | virus A/Finland/218/1992 1992. 1.4438 -3.7331 na 148 | virus A/Geneva/5113/1992 1992. 0.1868 -2.5623 na 149 | virus A/Houston/56798/1992 1992. 0.4922 -3.6022 na 150 | virus A/Houston/56829/1992 1992. 0.884 -1.3317 na 151 | virus A/Houston/56941/1992 1992. 1.9508 -2.1801 na 152 | virus A/Nijmegen/3126/1992 1992. 0.1754 -2.815 na 153 | virus A/Netherlands/823/1992 1992. 1.1093 -2.5336 na 154 | virus A/Paris/320/1992 1992. 0.7601 -2.8268 na 155 | virus A/Paris/325/1992 1992. 1.1199 -2.8509 na 156 | virus A/Paris/407/1992 1992. 0.8421 -3.7371 na 157 | virus A/Paris/417/1992 1992. 2.7321 -1.8958 na 158 | virus A/Paris/424/1992 1992. 0.5882 -2.9005 na 159 | virus A/Paris/457/1992 1992. -0.3142 -2.7946 na 160 | virus A/Paris/490/1992 1992. 1.5339 -2.1488 na 161 | virus A/Paris/512/1992 1992. 0.1833 -3.4838 na 162 | virus A/Paris/548/1992 1992. -0.7129 -4.7806 na 163 | virus A/Paris/564/1992 1992. 1.8374 -0.7847 na 164 | virus A/Paris/597/1992 1992. 1.8991 -3.3096 na 165 | virus A/Rotterdam/100540/1992 1992. 0.4168 -2.0848 na 166 | virus A/Stockholm/8/1992 1992. 1.0735 -2.2924 na 167 | virus A/Madrid/G102/1993 1993. 4.7211 3.0366 na 168 | virus A/Madrid/G252/1993 1993. 6.8542 -0.7801 na 169 | virus A/Akita/4/1993 1993. 5.0757 5.8519 na 170 | virus A/Enschede/5458/1993 1993. 3.0869 -1.3129 na 171 | virus A/Madrid/G101/1993 1993. 0.0113 -1.8785 na 172 | virus A/Madrid/G109/1993 1993. 4.3329 3.3014 na 173 | virus A/Madrid/G116/1993 1993. 0.8431 -3.3694 na 174 | virus A/Madrid/G122/1993 1993. 5.5324 2.16 na 175 | virus A/Madrid/G130/1993 1993. 3.8893 4.0763 na 176 | virus A/Netherlands/3/1993 1993. 3.6039 1.0152 na 177 | virus A/Netherlands/17/1993 1993. 3.1372 1.9826 na 178 | virus A/Netherlands/101/1993 1993. 3.1477 4.8135 na 179 | virus A/Netherlands/115/1993 1993. 3.8478 3.8233 na 180 | virus A/Netherlands/126/1993 1993. 3.1194 5.1485 na 181 | virus A/Netherlands/165/1993 1993. 1.345 -4.0342 na 182 | virus A/Netherlands/179/1993 1993. 2.9954 2.6572 na 183 | virus A/Paris/287/1993 1993. 2.3054 -1.8797 na 184 | virus A/Shiga/6/1993 1993. 5.8276 4.5059 na 185 | virus A/Yamagata/56/1993 1993. 6.3941 4.9043 na 186 | virus A/Yamagata/61/1993 1993. 4.6594 6.3995 na 187 | virus A/Yamagata/62/1993 1993. 5.0699 6.0709 na 188 | virus A/Netherlands/399/1993 1993. 5.942 -0.0446 na 189 | virus A/Shangdong/9/1993 1993. 5.252 5.0132 na 190 | virus A/Lyon/672/1993 1993. 4.1652 3.9937 na 191 | virus A/Lyon/1803/1993 1993. 4.5927 1.619 na 192 | virus A/Netherlands/357/1993 1993. 4.8301 3.1619 na 193 | virus A/Netherlands/371/1993 1993. 5.229 4.279 na 194 | virus A/Netherlands/372/1993 1993. 6.3995 -0.8271 na 195 | virus A/Netherlands/398/1993 1993. 4.4365 1.7325 na 196 | virus A/Netherlands/440/1993 1993. 4.7587 2.0663 na 197 | virus A/Oslow/2219/1993 1993. 5.7372 1.9894 na 198 | virus A/Oslow/2352/1993 1993. 4.8642 4.3528 na 199 | virus A/Stockholm/20/1993 1993. 5.4819 0.9647 na 200 | virus A/Victoria/104/1993 1993. 4.2051 4.2856 na 201 | virus A/Wellington/59/1993 1993. 6.1987 2.8953 na 202 | virus A/Singapore/19/1993 1993. 6.8149 -1.2784 na 203 | virus A/Lyon/1815/1993 1993. 6.0094 2.883 na 204 | virus A/Lyon/22686/1993 1993. 4.6561 4.1012 na 205 | virus A/Lyon/23602/1993 1993. 5.3572 1.9997 na 206 | virus A/Singapore/3/1993 1993. 4.2979 4.1216 na 207 | virus A/Guangdong/25/1993 1993. 6.9114 4.1815 na 208 | virus A/Scotland/142/1993 1993. 3.2201 3.3337 na 209 | virus A/Scotland/160/1993 1993. 5.2368 3.883 na 210 | virus A/HongKong/1/1994 1994. 5.3558 0.9896 na 211 | virus A/HongKong/2/1994 1994. 5.1606 -0.0432 na 212 | virus A/HongKong/56/1994 1994. 5.7811 1.4795 na 213 | virus A/SouthAustralia/15/1994 1994. 5.2667 1.8611 na 214 | virus A/SouthAustralia/25/1994 1994. 5.9781 2.0262 na 215 | virus A/Netherlands/18/1994 1994. 4.9469 1.4583 na 216 | virus A/Finland/338/1995 1995. 6.4901 -0.7597 na 217 | virus A/Stockholm/506/1995 1995. 5.9295 -0.221 na 218 | virus A/Geneva/AI9509/1995 1995. 4.9254 -0.53 na 219 | virus A/Finland/339/1995 1995. 9.8047 0.2916 na 220 | virus A/HongKong/3/1995 1995. 5.7988 1.9447 na 221 | virus A/Finland/381/1995 1995. 6.9287 -0.9952 na 222 | virus A/HongKong/38/1995 1995. 5.9309 1.2132 na 223 | virus A/HongKong/49/1995 1995. 7.0559 -0.4923 na 224 | virus A/HongKong/55/1995 1995. 6.3512 -0.3144 na 225 | virus A/Lyon/2279/1995 1995. 5.8031 -0.555 na 226 | virus A/Nanchang/933/1995 1995. 6.6316 -0.7586 na 227 | virus A/Netherlands/271/1995 1995. 9.3084 0.1568 na 228 | virus A/Victoria/75/1995 1995. 5.3241 0.7919 na 229 | virus A/Wuhan/359/1995 1995. 6.4035 -2.0379 na 230 | virus A/Brisbane/8/1996 1996. 7.0419 -3.4032 na 231 | virus A/Geneva/3958/1996 1996. 7.2874 -0.884 na 232 | virus A/HongKong/20/1996 1996. 7.0094 -1.7001 na 233 | virus A/HongKong/42/1996 1996. 6.8918 2.7114 na 234 | virus A/HongKong/357/1996 1996. 6.1172 -0.7105 na 235 | virus A/HongKong/358/1996 1996. 7.3762 -2.4445 na 236 | virus A/HongKong/434/1996 1996. 6.2736 5.0372 na 237 | virus A/Netherlands/91/1996 1996. 5.9058 3.1376 na 238 | virus A/Singapore/1/1996 1996. 6.3163 -1.1448 na 239 | virus A/Lyon/1781/1996 1996. 7.0865 -0.8012 na 240 | virus A/HongKong/1/1997 1997. 6.8902 -2.4476 na 241 | virus A/Nice/491/1997 1997. 8.2899 -2.4576 na 242 | virus A/Auckland/10/1997 1997. 11.1285 -4.7551 na 243 | virus A/HongKong/280/1997 1997. 8.0819 -2.9152 na 244 | virus A/Netherlands/300/1997 1997. 10.4808 -4.135 na 245 | virus A/Sydney/5/1997 1997. 12.2639 -3.7621 na 246 | virus A/Johannesburg/10/1997 1997. 6.3281 -2.1973 na 247 | virus A/Oslow/21/1997 1997. 7.0054 -1.2378 na 248 | virus A/Oslow/244/1997 1997. 6.8921 -1.1776 na 249 | virus A/Netherlands/5/1998 1998. 5.9783 -1.6786 na 250 | virus A/Netherlands/414/1998 1998. 9.8961 -2.7043 na 251 | virus A/Netherlands/462/1998 1998. 10.871 -2.2307 na 252 | virus A/Netherlands/427/1998 1998. 12.3106 -3.574 na 253 | virus A/Moscow/10/1999 1999. 9.4526 -4.2879 na 254 | virus A/Netherlands/301/1999 1999. 12.5834 -2.0606 na 255 | virus A/Panama/2007/1999 1999. 10.497 -2.7414 na 256 | virus A/Netherlands/3/2000 2000. 11.6397 -4.172 na 257 | virus A/Netherlands/118/2001 2001. 10.9346 -2.6596 na 258 | virus A/Netherlands/126/2001 2001. 10.8287 -0.8104 na 259 | virus A/Netherlands/124/2001 2001. 11.3649 -0.0696 na 260 | virus A/Netherlands/1/2002 2002. 12.2032 0.532 na 261 | virus A/Netherlands/120/2002 2002. 11.2973 -2.423 na 262 | virus A/Fujian/411/2002 2002. 15.6294 -0.8956 na 263 | virus A/Netherlands/22/2003 2003. 13.5285 2.3859 na 264 | virus A/Netherlands/213/2003 2003. 13.2986 -0.332 na 265 | virus A/Netherlands/217/2003 2003. 14.9817 -1.1646 na 266 | virus A/Netherlands/222/2003 2003. 13.3198 0.1649 na 267 | virus A/Finland/170/2003 2003. 13.9947 -0.6756 na 268 | virus A/Netherlands/20/2003 2003. 10.8874 -1.3408 na 269 | virus AL/4382/82 1982. -7.3292 2.1759 na 270 | virus OK/5/88 1988. -4.6413 -2.8448 na 271 | virus AT/3572DASH5/88 1988. -2.1848 0.5346 na 272 | virus EI/3447/89 1989. -1.9417 0.2794 na 273 | virus WK/1/89 1989. -1.5833 1.1101 na 274 | virus OV/31/92 1992. 0.898 -1.2266 na 275 | serum CC/4/85 1985. -7.1828 0.9922 10.1293 276 | serum NL/330/85 1985. -5.3347 0.651 11.3219 277 | serum NL/450/88 1988. -2.5302 0.5961 13.3219 278 | serum WE/4/85 1985. -3.8968 0.3842 12.3219 279 | serum PR/413/94 1994. 5.8467 1.6733 11.3219 280 | serum TE/1A/77 1977. -8.3861 1.811 10.9887 281 | serum PH/2/82 1982. -7.2922 3.7063 12.3219 282 | serum VI/7/87 1987. -2.1211 -1.2036 11.3219 283 | serum SI/2/87 1987. -2.6892 1.5978 11.9887 284 | serum EN/496/80 1980. -7.0232 3.5875 12.3219 285 | serum HK/1/68 1968. -17.6963 -2.6982 10.3219 286 | serum EN/42/72 1972. -15.2145 -2.9073 12.3219 287 | serum PC/1/73 1973. -13.3618 -0.6617 11.3219 288 | serum VI/3A/75 1975. -11.4521 -0.3454 11.3219 289 | serum LE/360/86 1986. -5.8062 2.1606 11.3219 290 | serum BA/1/79 1979. -6.8371 4.4673 10.3219 291 | serum SL/840/74 1974. -13.9329 -3.4594 11.3219 292 | serum BI/21793/72 1972. -16.8283 0.0863 10.3219 293 | serum BI/5930/74 1974. -14.0562 -0.8586 10.3219 294 | serum AM/1609/77 1977. -8.6615 -2.0482 11.3219 295 | serum BI/2461/78 1978. -7.6144 2.8472 11.8218 296 | serum RD/577/80 1980. -6.7269 4.5454 12.3219 297 | serum NL/209/80 1980. -8.1696 3.1354 12.3219 298 | serum NL/233/82 1982. -8.1555 2.4763 11.3219 299 | serum NL/241/82 1982. -7.9114 2.006 12.3219 300 | serum ST/10/85 1985. -4.4752 -0.1779 11.8218 301 | serum VI/2/90 1990. -0.2238 -2.4465 12.3219 302 | serum LY/1149/91 1991. 1.3974 -1.4015 11.3219 303 | serum MA/G252/93 1993. 6.5556 0.7333 10.0715 304 | serum NL/1/95 1995. 7.4111 3.3451 12.3219 305 | serum NL/218/95 1995. 7.2947 2.1864 11.7065 306 | serum NL/172/96 1996. 8.0592 -0.2738 11.3219 307 | serum TE/1B/77 1977. -9.1571 2.9605 13.3219 308 | serum BA/2/79 1979. -6.6847 1.9406 11.3219 309 | serum CE/1B/84 1984. -5.0423 0.281 9.3219 310 | serum CO/2/86 1986. -3.5704 -0.414 13.3219 311 | serum BE/353/89 1989. 0.2222 -0.6022 12.3219 312 | serum VI/3C/75 1975. -9.4982 -2.0007 11.3219 313 | serum SH/11/87 1987. -2.9194 1.9494 13.3219 314 | serum GD/25/93 1993. 3.0805 0.6764 12.9069 315 | serum JO/33/94 1994. 8.086 3.3006 12.9069 316 | serum NL/47/95 1995. 7.683 1.0137 10.9069 317 | serum NA/933/95 1995. 9.0439 -0.6937 10.3219 318 | serum LY/2279/95 1995. 8.2155 1.1446 12.1293 319 | serum SP/1/96 1996. 5.6625 -2.4515 11.5718 320 | serum AU/10/97 1997. 10.0677 -2.6615 12.1144 321 | serum NL/5/98 1998. 8.569 -0.4741 12.3219 322 | serum NL/18/94 1994. 8.7772 0.2682 11.9069 323 | serum HK/107/71 1971. -19.991 0.2877 12.3219 324 | serum PH/2V/82 1982. -8.7511 4.7826 11.2761 325 | serum BE/32V/92 1992. 3.4405 6.2235 10.0941 326 | serum NL/286/97 1997. 5.8246 -1.6843 9.9069 327 | serum SY/5V/97 1997. 11.2192 -4.57 12.9069 328 | serum GU/54/89 1989. -1.2453 -0.1559 13.3219 329 | serum NL/333/85 1985. -5.6863 1.3992 10.3219 330 | serum CE/1A/84 1984. -6.0094 1.7253 10.3219 331 | serum SH/31/80 1980. -7.541 0.9062 9.9069 332 | serum NL/620/89 1989. -1.2441 0.1824 14.3219 333 | serum BE/32A/92 1992. 4.0971 2.2012 10.4828 334 | serum HK/34/90 1990. 0.7629 2.1479 13.3219 335 | serum BE/32B/92 1992. 3.349 2.129 9.8218 336 | serum FI/338/95 1995. 7.6545 2.1832 13.3219 337 | serum SD/9/93 1993. 5.0346 2.4406 12.1293 338 | serum OS/2352/93 1993. 5.0386 2.0578 10.8796 339 | serum GE/A9509/95 1995. 6.1128 1.3676 11.4681 340 | serum BR/8/96 1996. 7.5707 -0.9828 11.5718 341 | serum SY/5B/97 1997. 11.1228 -3.229 12.9069 342 | serum SY/5A/97 1997. 11.1327 -2.7173 11.9894 343 | serum WU/359B/95 1995. 7.0134 -0.7379 11.3219 344 | serum MW/10/99 1999. 11.6824 -2.1117 11.7752 345 | serum SY/5HAY/97 1997. 12.6182 -2.9599 11.9069 346 | serum NL/1/02 2002. 11.666 -1.7195 11.3219 347 | serum PM/2007/99 1999. 11.8152 -1.869 11.7258 348 | serum NL/126/01 2001. 11.7236 -2.7368 11.3219 349 | serum NL/118/01 2001. 12.0336 -2.226 11.5182 350 | serum FU/411/02 2002. 14.923 0.8892 12.9885 351 | serum NL/88/03 2003. 12.3008 -1.9664 11.9069 352 | serum NL/22/03 2003. 14.3421 -0.2636 12.5365 353 | serum NL/124/01 2001. 12.133 -1.7566 11.9069 -------------------------------------------------------------------------------- /figure-data/fig12_smith_mds_effects.tsv: -------------------------------------------------------------------------------- 1 | type name year ag1 ag2 avidity_or_potency 2 | virus A/Rotterdam/577/1980 1980. -7.5046 -2.6104 12.9049 3 | virus A/ChristChurch/2/1988 1988. -4.4589 -2.4216 10.8823 4 | virus A/Netherlands/241/1993 1993. 6.118 4.0594 12.3882 5 | virus A/HongKong/55/1994 1994. 6.6946 3.1087 12.4941 6 | virus A/England/7/1994 1994. 9.0821 2.7325 11.515 7 | virus A/Johannesburg/33/1994 1994. 6.2443 4.284 10.9052 8 | virus A/Johannesburg/47/1994 1994. 7.1756 4.6723 10.9619 9 | virus A/Netherlands/1/1995 1995. 6.6456 4.1348 11.9382 10 | virus A/HongKong/32/1995 1995. 5.552 3.5486 12.4716 11 | virus A/Bilthoven/15793/1968 1968. -17.2216 -2.354 10.9029 12 | virus A/Bilthoven/16190/1968 1968. -17.3332 1.6738 11.2262 13 | virus A/Bilthoven/16398/1968 1968. -18.6798 0.0528 11.6369 14 | virus A/HongKong/1/1968 1968. -19.9868 3.6069 12.0594 15 | virus A/Bilthoven/808/1969 1969. -17.0715 -3.3959 11.0632 16 | virus A/Bilthoven/908/1969 1969. -17.8409 2.6512 11.5689 17 | virus A/Bilthoven/17938/1969 1969. -17.374 4.2831 11.077 18 | virus A/Bilthoven/93/1970 1970. -18.018 2.8715 11.4173 19 | virus A/Bilthoven/2668/1970 1970. -17.7341 -1.5166 10.9197 20 | virus A/Bilthoven/6449/1971 1971. -17.7791 -2.1258 10.651 21 | virus A/Bilthoven/21438/1971 1971. -18.2742 -0.5451 11.3224 22 | virus A/Bilthoven/21801/1971 1971. -18.0975 2.0668 11.4394 23 | virus A/HongKong/107/1971 1971. -17.614 3.4823 13.3606 24 | virus A/Bilthoven/6022/1972 1972. -16.5575 -0.3705 11.4241 25 | virus A/Bilthoven/21793/1972 1972. -14.9821 1.5978 11.1822 26 | virus A/Bilthoven/23290/1972 1972. -13.8705 3.1266 10.8249 27 | virus A/Bilthoven/23337/1972 1972. -14.1999 2.6462 10.8079 28 | virus A/England/42/1972 1972. -16.3665 0.3457 11.4817 29 | virus A/Bilthoven/552/1973 1973. -13.4707 1.8015 11.4371 30 | virus A/Bilthoven/748/1973 1973. -14.6371 4.1903 10.6515 31 | virus A/Bilthoven/3517/1973 1973. -14.225 3.7412 10.9356 32 | virus A/PortChalmers/1/1973 1973. -13.7155 -2.2929 10.4987 33 | virus A/Bilthoven/5146/1974 1974. -14.0944 3.0357 10.2913 34 | virus A/Bilthoven/5930/1974 1974. -13.919 3.3579 10.9691 35 | virus A/Bilthoven/5931/1974 1974. -14.0967 -1.9674 9.559 36 | virus A/Bilthoven/7398/1974 1974. -13.838 0.2759 10.2747 37 | virus A/Bilthoven/9459/1974 1974. -13.7753 1.2443 10.4452 38 | virus A/Bilthoven/4273/1975 1975. -13.8466 3.591 10.4297 39 | virus A/Bilthoven/334/1975 1975. -14.8808 0.7499 9.214 40 | virus A/Bilthoven/1843/1975 1975. -13.138 3.4286 10.9223 41 | virus A/Bilthoven/2600/1975 1975. -14.5925 1.6916 11.14 42 | virus A/Bilthoven/2813/1975 1975. -13.9335 3.8616 11.2744 43 | virus A/Victoria/3/1975 1975. -12.213 -1.4382 11.7865 44 | virus A/Bilthoven/5168/1976 1976. -11.7619 -0.9748 10.532 45 | virus A/Bilthoven/628/1976 1976. -9.3433 -2.2372 11.9695 46 | virus A/Bilthoven/1761/1976 1976. -11.764 -3.8636 11.9754 47 | virus A/Bilthoven/2271/1976 1976. -9.2066 0.2137 12.7932 48 | virus A/Bilthoven/5029/1976 1976. -12.0255 -3.5546 11.5242 49 | virus A/Bilthoven/5657/1976 1976. -11.2563 -3.1653 11.6734 50 | virus A/Bilthoven/6545/1976 1976. -11.0876 -2.8452 12.1703 51 | virus A/Amsterdam/1609/1977 1977. -11.7756 -2.0264 12.3373 52 | virus A/Bilthoven/3895/1977 1977. -11.4 -3.4814 12.438 53 | virus A/Rotterdam/5828/1977 1977. -13.0788 -3.0927 12.6781 54 | virus A/Rotterdam/8179/1977 1977. -13.0812 -3.7266 13.2668 55 | virus A/Texas/1/1977 1977. -9.2642 -2.0587 11.6077 56 | virus A/Bangkok/1/1979 1979. -6.9084 -1.1897 9.0254 57 | virus A/Netherlands/209/1980 1980. -7.6283 -2.1409 12.8386 58 | virus A/Lyon/2380/1981 1981. -6.3444 -0.2346 13.7163 59 | virus A/Bilthoven/4791/1981 1981. -5.9641 0.4197 11.9684 60 | virus A/Netherlands/233/1982 1982. -7.3974 -3.0381 11.6877 61 | virus A/Netherlands/241/1982 1982. -7.0016 -2.9848 11.6993 62 | virus A/Bilthoven/10684/1982 1982. -6.623 -0.3483 12.307 63 | virus A/Philippines/2/1982 1982. -5.8972 -3.3169 10.4242 64 | virus A/Oslow/13676/1983 1983. -6.7039 -0.849 12.7161 65 | virus A/Caen/1/1984 1984. -5.0376 1.1764 10.8015 66 | virus A/Netherlands/330/1985 1985. -5.8471 -3.0267 10.853 67 | virus A/Stockholm/10/1985 1985. -5.6247 -3.8936 12.3615 68 | virus A/Wellington/4/1985 1985. -4.5046 -2.074 11.7521 69 | virus A/Netherlands/333/1985 1985. -5.2127 3.1706 11.3139 70 | virus A/Guildford/V728/1985 1985. -3.9357 -2.7005 10.9862 71 | virus A/Colorado/2/1986 1986. -5.2663 -3.2668 12.3522 72 | virus A/Leningrad/360/1986 1986. -4.7085 -2.3458 8.855 73 | virus A/Sichuan/2/1987 1987. -2.9923 2.0699 10.5862 74 | virus A/Victoria/7/1987 1987. -2.352 -3.0122 11.229 75 | virus A/Shanghai/11/1987 1987. -2.3612 0.5178 7.9063 76 | virus A/Netherlands/450/1988 1988. -2.0455 0.8557 12.2377 77 | virus A/Victoria/1/1988 1988. -2.7762 -3.2477 10.7781 78 | virus A/Stockholm/12/1988 1988. -2.1292 1.1218 12.9153 79 | virus A/England/427/1988 1988. -2.5361 1.6953 11.3636 80 | virus A/Netherlands/620/1989 1989. -1.8883 1.45 11.5551 81 | virus A/England//1989 1989. -1.1151 2.3281 12.108 82 | virus A/Geneva/5007/1989 1989. -2.4154 0.7738 12.5375 83 | virus A/Guizhou/54/1989 1989. -2.584 5.3052 11.3753 84 | virus A/HongKong/1/1989 1989. -2.3869 0.9025 12.5797 85 | virus A/Netherlands/650/1989 1989. -0.8431 3.2668 11.6831 86 | virus A/Netherlands/738/1989 1989. -1.6183 3.6446 11.1068 87 | virus A/Singapore/35/1989 1989. -1.4016 1.1366 11.6369 88 | virus A/Singapore/40/1989 1989. -0.0166 0.5603 11.7481 89 | virus A/Wellington/5/1989 1989. -2.5018 1.503 11.0555 90 | virus A/Beijing/353/1989 1989. 0.0532 -1.5666 8.5248 91 | virus A/Beijing/352/1989 1989. 1.8006 -0.6445 10.3553 92 | virus A/Atlanta/211/1989 1989. -0.0839 -1.7247 11.5678 93 | virus A/Singapore/34/1989 1989. -0.3742 1.2395 11.3174 94 | virus A/Singapore/36/1989 1989. -0.15 1.0172 11.1309 95 | virus A/Singapore/53/1989 1989. -0.6353 1.5667 11.3031 96 | virus A/Victoria/1/1989 1989. -1.9146 3.5673 10.8842 97 | virus A/Victoria/2/1990 1990. 0.7105 -1.193 11.0406 98 | virus A/Wellington/3/1990 1990. 0.7174 -2.4382 11.1258 99 | virus A/Memphis/2/1990 1990. -1.7035 3.1677 12.2494 100 | virus A/Seoul/1/1990 1990. -1.593 1.7162 12.6134 101 | virus A/Memphis/5/1990 1990. -0.2056 0.2972 11.558 102 | virus A/Shanghai/24/1990 1990. 0.7053 2.5907 11.5567 103 | virus A/Lyon/1149/1991 1991. 2.4941 -2.7276 12.755 104 | virus A/Netherlands/891/1991 1991. 0.6265 -1.9283 11.1829 105 | virus A/Canberra/1/1991 1991. -2.2878 0.3348 12.2076 106 | virus A/England/260/1991 1991. 0.3891 -3.4567 11.4286 107 | virus A/England/261/1991 1991. 2.2828 -0.1668 10.9192 108 | virus A/Madrid/G12/1991 1991. 0.9711 -2.0009 10.8834 109 | virus A/Netherlands/816/1991 1991. 0.0453 -2.5596 10.9165 110 | virus A/Geneva/5366/1991 1991. -2.3825 -0.5579 11.3772 111 | virus A/Lyon/1182/1991 1991. 2.1955 -3.4784 11.9641 112 | virus A/Geneva/6447/1991 1991. 1.629 -3.7262 10.9652 113 | virus A/Lyon/1189/1991 1991. 0.8833 -1.5625 11.1337 114 | virus A/Lyon/1276/1991 1991. 2.3962 -1.3982 11.6957 115 | virus A/Lyon/1337/1991 1991. 1.7531 -2.6981 11.1941 116 | virus A/Lyon/1373/1991 1991. 1.5799 -2.9397 10.9858 117 | virus A/Lyon/1594/1991 1991. 0.8721 -3.0006 10.7436 118 | virus A/Lyon/23672/1991 1991. 1.4381 -1.9701 10.5971 119 | virus A/Lyon/24103/1991 1991. 0.8549 -1.8349 11.7039 120 | virus A/Lyon/24222/1991 1991. 2.2278 -2.421 11.743 121 | virus A/Stockholm/20/1991 1991. 0.7067 -2.3714 10.9228 122 | virus A/Victoria/33/1992 1992. 0.2262 -1.5258 11.4671 123 | virus A/Amsterdam/4112/1992 1992. 0.3325 -2.6753 11.7582 124 | virus A/Enschede/1285/1992 1992. 0.3609 -2.1557 10.8314 125 | virus A/Finland/220/1992 1992. 1.8581 0.8483 9.6909 126 | virus A/Madrid/G58/1992 1992. 0.6678 -3.2373 12.1401 127 | virus A/Nijmegen/3129/1992 1992. 1.2017 -2.3389 11.1266 128 | virus A/Netherlands/819/1992 1992. 1.8652 -2.2913 12.1196 129 | virus A/Netherlands/935/1992 1992. 0.6382 -2.6168 12.0026 130 | virus A/Paris/583/1992 1992. 0.7625 -2.1311 10.4404 131 | virus A/Paris/614/1992 1992. 0.1139 -3.2697 11.7254 132 | virus A/SouthAustralia/8/1992 1992. 1.7398 -2.5247 10.5189 133 | virus A/SouthAustralia/23/1992 1992. 0.0622 -1.994 10.4069 134 | virus A/SouthAustralia/27/1992 1992. 2.2066 -2.0216 10.4756 135 | virus A/Stockholm/7/1992 1992. 0.0591 -2.5486 10.1058 136 | virus A/Victoria/68/1992 1992. 0.4373 -1.6337 12.2664 137 | virus A/Paris/467/1992 1992. -0.6249 -2.8529 11.5536 138 | virus A/Tilburg/5957/1992 1992. 0.5948 -2.8773 11.7778 139 | virus A/Beijing/32/1992 1992. 2.5291 2.0799 9.9357 140 | virus A/Finland/247/1992 1992. 4.3463 6.6075 10.8377 141 | virus A/Netherlands/938/1992 1992. 1.2476 3.7762 12.7441 142 | virus A/Sendai/C273/1992 1992. 3.927 4.8693 9.0264 143 | virus A/Stockholm/12/1992 1992. 4.06 3.4708 11.6299 144 | virus A/Stockholm/13/1992 1992. -0.6024 -1.5629 11.5295 145 | virus A/Umea/1982/1992 1992. 0.296 -3.6734 10.7516 146 | virus A/Umea/2000/1992 1992. 0.9384 -3.0112 10.8138 147 | virus A/Finland/218/1992 1992. 1.7755 -3.3192 10.5118 148 | virus A/Geneva/5113/1992 1992. -0.0736 -2.9283 9.8582 149 | virus A/Houston/56798/1992 1992. 0.9585 -3.2714 10.3011 150 | virus A/Houston/56829/1992 1992. 1.4751 -2.2264 11.3002 151 | virus A/Houston/56941/1992 1992. 1.1596 -1.6812 10.904 152 | virus A/Nijmegen/3126/1992 1992. 0.624 -1.6988 10.8688 153 | virus A/Netherlands/823/1992 1992. 1.3966 -2.498 10.93 154 | virus A/Paris/320/1992 1992. 0.1515 -3.2031 11.1738 155 | virus A/Paris/325/1992 1992. 0.1042 -3.5409 10.5415 156 | virus A/Paris/407/1992 1992. 0.4537 -2.9917 10.3259 157 | virus A/Paris/417/1992 1992. 2.5684 -1.3653 12.3843 158 | virus A/Paris/424/1992 1992. 1.4528 -2.4346 11.069 159 | virus A/Paris/457/1992 1992. -0.5875 -2.7022 10.1093 160 | virus A/Paris/490/1992 1992. 0.904 -2.5722 11.0275 161 | virus A/Paris/512/1992 1992. 0.6959 -2.6222 10.5443 162 | virus A/Paris/548/1992 1992. 0.2217 -3.8552 9.7804 163 | virus A/Paris/564/1992 1992. 2.4274 -1.6336 12.187 164 | virus A/Paris/597/1992 1992. 2.2358 -2.061 10.9516 165 | virus A/Rotterdam/100540/1992 1992. 0.7897 -2.3686 11.4664 166 | virus A/Stockholm/8/1992 1992. 2.2413 -2.401 10.8193 167 | virus A/Madrid/G102/1993 1993. 4.7912 2.9009 11.0945 168 | virus A/Madrid/G252/1993 1993. 7.167 0.7969 10.405 169 | virus A/Akita/4/1993 1993. 5.3061 5.0491 10.3222 170 | virus A/Enschede/5458/1993 1993. 3.2751 -3.1461 12.2537 171 | virus A/Madrid/G101/1993 1993. 0.3201 -3.246 11.0113 172 | virus A/Madrid/G109/1993 1993. 4.5996 3.6562 12.3511 173 | virus A/Madrid/G116/1993 1993. 0.8021 -3.3171 10.5238 174 | virus A/Madrid/G122/1993 1993. 6.2227 4.2589 13.8749 175 | virus A/Madrid/G130/1993 1993. 3.134 4.7127 10.9932 176 | virus A/Netherlands/3/1993 1993. 3.991 3.8472 13.4455 177 | virus A/Netherlands/17/1993 1993. 2.3913 1.7329 11.2298 178 | virus A/Netherlands/101/1993 1993. 2.3224 4.5616 10.9038 179 | virus A/Netherlands/115/1993 1993. 3.2022 4.9635 10.9778 180 | virus A/Netherlands/126/1993 1993. 2.7239 4.4761 11.0337 181 | virus A/Netherlands/165/1993 1993. 1.0139 -4.49 10.1679 182 | virus A/Netherlands/179/1993 1993. 4.3417 2.9986 11.0581 183 | virus A/Paris/287/1993 1993. 0.5496 -3.7251 10.8678 184 | virus A/Shiga/6/1993 1993. 4.8525 3.8418 10.0276 185 | virus A/Yamagata/56/1993 1993. 5.3433 2.8923 9.549 186 | virus A/Yamagata/61/1993 1993. 5.1174 6.0967 9.9096 187 | virus A/Yamagata/62/1993 1993. 5.0431 3.8635 10.146 188 | virus A/Netherlands/399/1993 1993. 6.6871 -0.2503 10.0069 189 | virus A/Shangdong/9/1993 1993. 4.5613 4.1631 9.3197 190 | virus A/Lyon/672/1993 1993. 4.9934 4.016 10.3934 191 | virus A/Lyon/1803/1993 1993. 4.256 5.9073 10.99 192 | virus A/Netherlands/357/1993 1993. 4.5496 3.5136 11.4339 193 | virus A/Netherlands/371/1993 1993. 6.2459 5.6762 10.944 194 | virus A/Netherlands/372/1993 1993. 8.9131 1.8069 10.2244 195 | virus A/Netherlands/398/1993 1993. 5.5408 2.3527 12.8526 196 | virus A/Netherlands/440/1993 1993. 4.9421 2.5601 11.2624 197 | virus A/Oslow/2219/1993 1993. 6.0816 3.3505 12.2153 198 | virus A/Oslow/2352/1993 1993. 3.8271 4.9371 10.4847 199 | virus A/Stockholm/20/1993 1993. 6.6218 3.7184 12.3494 200 | virus A/Victoria/104/1993 1993. 4.0322 3.2744 10.413 201 | virus A/Wellington/59/1993 1993. 5.1788 3.7681 11.2638 202 | virus A/Singapore/19/1993 1993. 7.337 -1.2988 10.3934 203 | virus A/Lyon/1815/1993 1993. 7.4804 4.3231 12.3605 204 | virus A/Lyon/22686/1993 1993. 5.46 2.9515 11.3399 205 | virus A/Lyon/23602/1993 1993. 5.5564 3.0377 12.1583 206 | virus A/Singapore/3/1993 1993. 4.584 3.1854 10.2681 207 | virus A/Guangdong/25/1993 1993. 6.2544 5.7898 11.3392 208 | virus A/Scotland/142/1993 1993. 3.2259 5.7551 11.4337 209 | virus A/Scotland/160/1993 1993. 6.8508 4.2723 11.389 210 | virus A/HongKong/1/1994 1994. 6.459 3.5565 11.5319 211 | virus A/HongKong/2/1994 1994. 4.2237 3.4528 10.8469 212 | virus A/HongKong/56/1994 1994. 6.9175 4.1328 12.7117 213 | virus A/SouthAustralia/15/1994 1994. 6.012 3.4193 12.6221 214 | virus A/SouthAustralia/25/1994 1994. 6.427 4.0127 12.693 215 | virus A/Netherlands/18/1994 1994. 5.6116 2.2253 9.7181 216 | virus A/Finland/338/1995 1995. 7.0402 1.3769 10.6575 217 | virus A/Stockholm/506/1995 1995. 7.0653 4.7588 10.4597 218 | virus A/Geneva/AI9509/1995 1995. 5.9064 1.9561 9.0943 219 | virus A/Finland/339/1995 1995. 10.7533 1.9411 11.2669 220 | virus A/HongKong/3/1995 1995. 5.6866 3.7634 11.6087 221 | virus A/Finland/381/1995 1995. 9.5673 2.3341 10.8505 222 | virus A/HongKong/38/1995 1995. 6.1085 2.1637 11.5387 223 | virus A/HongKong/49/1995 1995. 7.952 1.8396 11.4526 224 | virus A/HongKong/55/1995 1995. 5.6291 0.5825 12.3465 225 | virus A/Lyon/2279/1995 1995. 6.0889 0.6846 10.8979 226 | virus A/Nanchang/933/1995 1995. 6.351 -0.2705 11.266 227 | virus A/Netherlands/271/1995 1995. 8.7147 1.19 11.1268 228 | virus A/Victoria/75/1995 1995. 6.143 1.6473 10.7098 229 | virus A/Wuhan/359/1995 1995. 6.5704 -0.0909 10.7386 230 | virus A/Brisbane/8/1996 1996. 7.3302 -1.2962 10.832 231 | virus A/Geneva/3958/1996 1996. 6.8858 -0.9493 12.7753 232 | virus A/HongKong/20/1996 1996. 7.5934 -0.7954 12.2427 233 | virus A/HongKong/42/1996 1996. 7.0866 3.1367 10.1541 234 | virus A/HongKong/357/1996 1996. 7.2859 -0.25 11.7882 235 | virus A/HongKong/358/1996 1996. 6.9361 -0.6047 10.6458 236 | virus A/HongKong/434/1996 1996. 6.8042 5.5364 10.8826 237 | virus A/Netherlands/91/1996 1996. 5.0536 4.7994 11.1837 238 | virus A/Singapore/1/1996 1996. 6.3382 -0.1353 11.1758 239 | virus A/Lyon/1781/1996 1996. 5.9458 -1.3875 11.9661 240 | virus A/HongKong/1/1997 1997. 7.0449 -0.96 11.2311 241 | virus A/Nice/491/1997 1997. 5.3473 -2.1877 11.1799 242 | virus A/Auckland/10/1997 1997. 9.1632 -4.2482 12.0864 243 | virus A/HongKong/280/1997 1997. 7.3404 -1.1362 11.1305 244 | virus A/Netherlands/300/1997 1997. 9.2541 -3.0411 11.628 245 | virus A/Sydney/5/1997 1997. 10.2332 -5.1557 12.0462 246 | virus A/Johannesburg/10/1997 1997. 5.9555 -0.8653 11.4706 247 | virus A/Oslow/21/1997 1997. 6.9024 0.2159 11.7095 248 | virus A/Oslow/244/1997 1997. 6.5283 -0.6579 11.887 249 | virus A/Netherlands/5/1998 1998. 5.5831 -0.0097 11.4065 250 | virus A/Netherlands/414/1998 1998. 9.0532 -2.5339 12.3799 251 | virus A/Netherlands/462/1998 1998. 9.8051 -2.1369 12.2235 252 | virus A/Netherlands/427/1998 1998. 11.4021 -4.3393 11.5469 253 | virus A/Moscow/10/1999 1999. 8.6263 -4.5791 10.8172 254 | virus A/Netherlands/301/1999 1999. 10.1631 -2.1819 11.9647 255 | virus A/Panama/2007/1999 1999. 10.2495 -4.8288 12.1418 256 | virus A/Netherlands/3/2000 2000. 9.4332 -3.2079 10.8503 257 | virus A/Netherlands/118/2001 2001. 11.0374 -3.704 12.7368 258 | virus A/Netherlands/126/2001 2001. 10.731 -3.4465 11.411 259 | virus A/Netherlands/124/2001 2001. 11.346 -1.9324 11.8952 260 | virus A/Netherlands/1/2002 2002. 11.2927 -1.0805 11.2568 261 | virus A/Netherlands/120/2002 2002. 10.9088 -5.015 12.3443 262 | virus A/Fujian/411/2002 2002. 14.8524 -2.73 11.5541 263 | virus A/Netherlands/22/2003 2003. 14.1279 -0.3828 12.2347 264 | virus A/Netherlands/213/2003 2003. 14.2429 -1.5915 13.6351 265 | virus A/Netherlands/217/2003 2003. 14.1783 -2.558 12.2373 266 | virus A/Netherlands/222/2003 2003. 13.5557 -1.2996 13.0775 267 | virus A/Finland/170/2003 2003. 15.0001 -1.6942 12.8842 268 | virus A/Netherlands/20/2003 2003. 10.709 -1.8568 13.2056 269 | virus AL/4382/82 1982. -7.0782 0.605 14.0918 270 | virus OK/5/88 1988. -1.5274 -2.7146 10.5394 271 | virus AT/3572DASH5/88 1988. -2.9305 0.4507 12.5363 272 | virus EI/3447/89 1989. -1.7196 2.3707 12.1001 273 | virus WK/1/89 1989. -0.9592 1.9917 11.9322 274 | virus OV/31/92 1992. 0.4655 -2.2269 12.2309 275 | serum CC/4/85 1985. -4.5392 -1.0237 10.8209 276 | serum NL/330/85 1985. -5.471 -0.6533 13.4559 277 | serum NL/450/88 1988. -2.2504 0.2597 15.2812 278 | serum WE/4/85 1985. -4.3652 -0.2371 15.9639 279 | serum PR/413/94 1994. 7.1371 2.293 12.368 280 | serum TE/1A/77 1977. -8.2005 0.6551 12.1285 281 | serum PH/2/82 1982. -6.4905 -1.0915 11.0775 282 | serum VI/7/87 1987. -1.5893 -1.4852 12.5076 283 | serum SI/2/87 1987. -2.2978 0.8284 11.6041 284 | serum EN/496/80 1980. -6.5618 -1.1163 10.8073 285 | serum HK/1/68 1968. -19.667 1.0572 10.985 286 | serum EN/42/72 1972. -16.1901 0.3953 13.4521 287 | serum PC/1/73 1973. -13.4867 0.8695 13.5957 288 | serum VI/3A/75 1975. -12.6046 -0.8005 12.2872 289 | serum LE/360/86 1986. -5.137 -1.4761 12.2826 290 | serum BA/1/79 1979. -6.9324 -0.5286 6.8962 291 | serum SL/840/74 1974. -14.103 1.1667 10.193 292 | serum BI/21793/72 1972. -16.8982 0.8303 11.7142 293 | serum BI/5930/74 1974. -14.2734 1.2341 12.7932 294 | serum AM/1609/77 1977. -10.8305 -3.7172 10.8052 295 | serum BI/2461/78 1978. -6.5913 -1.8563 9.7451 296 | serum RD/577/80 1980. -7.4158 -2.2588 9.3858 297 | serum NL/209/80 1980. -7.5624 -3.535 11.3143 298 | serum NL/233/82 1982. -7.6506 -3.2525 10.4034 299 | serum NL/241/82 1982. -7.1219 -2.7494 12.1935 300 | serum ST/10/85 1985. -4.1177 -1.9602 15.0529 301 | serum VI/2/90 1990. 0.4702 -2.3182 12.4137 302 | serum LY/1149/91 1991. 1.7471 -2.2514 12.9834 303 | serum MA/G252/93 1993. 7.1514 1.5596 10.5052 304 | serum NL/1/95 1995. 6.8413 3.7888 11.736 305 | serum NL/218/95 1995. 7.5446 3.3949 12.3813 306 | serum NL/172/96 1996. 7.9857 0.2681 11.8814 307 | serum TE/1B/77 1977. -8.9849 0.959 15.2915 308 | serum BA/2/79 1979. -6.3846 -1.3681 11.1917 309 | serum CE/1B/84 1984. -6.4463 0.366 9.6978 310 | serum CO/2/86 1986. -4.196 -1.7369 18.0038 311 | serum BE/353/89 1989. 1.0416 -0.7389 13.066 312 | serum VI/3C/75 1975. -11.213 -2.8424 11.2985 313 | serum SH/11/87 1987. -2.4001 1.7718 14.6771 314 | serum GD/25/93 1993. 6.6363 3.8878 10.812 315 | serum JO/33/94 1994. 6.5452 3.5005 11.6114 316 | serum NL/47/95 1995. 7.5748 2.2031 10.4734 317 | serum NA/933/95 1995. 8.3823 -0.2905 9.3234 318 | serum LY/2279/95 1995. 7.7405 1.55 11.6204 319 | serum SP/1/96 1996. 6.4304 -0.9698 9.9457 320 | serum AU/10/97 1997. 10.4525 -3.0862 13.8142 321 | serum NL/5/98 1998. 6.4083 -0.4189 11.5912 322 | serum NL/18/94 1994. 8.7513 1.3745 11.3046 323 | serum HK/107/71 1971. -19.2641 5.8268 11.2553 324 | serum PH/2V/82 1982. -6.5012 -4.3445 11.0647 325 | serum BE/32V/92 1992. 2.1245 4.2076 10.2116 326 | serum NL/286/97 1997. 4.8293 -0.6926 10.3401 327 | serum SY/5V/97 1997. 9.5273 -4.4437 12.5055 328 | serum GU/54/89 1989. -1.8331 2.2811 13.0119 329 | serum NL/333/85 1985. -6.1283 0.2489 12.1795 330 | serum CE/1A/84 1984. -5.7053 0.7567 12.2508 331 | serum SH/31/80 1980. -7.8123 1.9313 10.7863 332 | serum NL/620/89 1989. -1.0872 -0.2372 17.2715 333 | serum BE/32A/92 1992. 3.4523 2.536 11.6241 334 | serum HK/34/90 1990. 1.9421 2.2874 14.1501 335 | serum BE/32B/92 1992. 2.9133 2.0725 11.17 336 | serum FI/338/95 1995. 6.0451 2.6981 12.9495 337 | serum SD/9/93 1993. 4.9587 3.0201 13.1716 338 | serum OS/2352/93 1993. 4.2799 3.0099 11.6977 339 | serum GE/A9509/95 1995. 7.2619 2.874 12.3187 340 | serum BR/8/96 1996. 6.7554 -0.0551 11.134 341 | serum SY/5B/97 1997. 9.4046 -3.8061 12.7148 342 | serum SY/5A/97 1997. 9.6878 -4.1283 12.1241 343 | serum WU/359B/95 1995. 6.0013 1.4578 11.7809 344 | serum MW/10/99 1999. 11.0989 -3.2065 11.7306 345 | serum SY/5HAY/97 1997. 10.0341 -5.0324 11.5375 346 | serum NL/1/02 2002. 9.9199 -2.3205 11.2543 347 | serum PM/2007/99 1999. 12.004 -3.4449 11.8319 348 | serum NL/126/01 2001. 9.4507 -3.2077 11.3592 349 | serum NL/118/01 2001. 10.6021 -3.0902 11.9864 350 | serum FU/411/02 2002. 14.5774 -1.5423 12.4793 351 | serum NL/88/03 2003. 11.6722 -2.5912 10.8137 352 | serum NL/22/03 2003. 14.1186 -1.8549 12.8515 353 | serum NL/124/01 2001. 11.5299 -4.0144 12.1511 -------------------------------------------------------------------------------- /data/H3N2_seq_data.tsv: -------------------------------------------------------------------------------- 1 | strain accession type subtype year database 2 | A/Akita/4/1993 EPI_ISL_115040 A H3N2 1993 GISAID 3 | A/Alabama/5/2010 EPI_ISL_81372 A H3N2 2010 GISAID 4 | A/Alaska/5/2010 EPI_ISL_88045 A H3N2 2010 GISAID 5 | A/Algeria/G202/2009 EPI_ISL_61769 A H3N2 2008 GISAID 6 | A/Amsterdam/1609/1977 EPI_ISL_114017 A H3N2 1977 GISAID 7 | A/Anhui/1238/2005 EPI_ISL_17358 A H3N2 2005 GISAID 8 | A/Anhui/1239/2005 EPI_ISL_17359 A H3N2 2005 GISAID 9 | A/Atlanta/211/1989 EPI_ISL_114345 A H3N2 1989 GISAID 10 | A/Atlanta/3572/1988 EPI_ISL_114295 A H3N2 1988 GISAID 11 | A/Auckland/10/1997 EPI_ISL_115568 A H3N2 1997 GISAID 12 | A/Auckland/4382/1982 CY116571 A H3N2 1982 IRD 13 | A/Auckland/6/2003 EU501205 A H3N2 2003 IRD 14 | A/BadenWuerttemberg/38/2005 EPI_ISL_64611 A H3N2 2005 GISAID 15 | A/Bangkok/1/1979 EPI_ISL_115698 A H3N2 1979 GISAID 16 | A/Bangladesh/5071/2011 EPI_ISL_99069 A H3N2 2011 GISAID 17 | A/Beijing/32/1992 EPI_ISL_114610 A H3N2 1992 GISAID 18 | A/Beijing/352/1989 EPI_ISL_110905 A H3N2 1989 GISAID 19 | A/Beijing/353/1989 EPI_ISL_115769 A H3N2 1989 GISAID 20 | A/Beijing/51/2002 EPI_ISL_18407 A H3N2 2002 GISAID 21 | A/Bilthoven/10684/1982 EPI_ISL_114200 A H3N2 1982 GISAID 22 | A/Bilthoven/15793/1968 EPI_ISL_110734 A H3N2 1968 GISAID 23 | A/Bilthoven/16190/1968 AY661039 A H3N2 1968 IRD 24 | A/Bilthoven/16398/1968 EPI_ISL_110745 A H3N2 1968 GISAID 25 | A/Bilthoven/1761/1976 EPI_ISL_84896 A H3N2 1976 GISAID 26 | A/Bilthoven/17938/1969 EPI_ISL_113035 A H3N2 1969 GISAID 27 | A/Bilthoven/1843/1975 EPI_ISL_113965 A H3N2 1975 GISAID 28 | A/Bilthoven/21438/1971 EPI_ISL_113036 A H3N2 1971 GISAID 29 | A/Bilthoven/21793/1972 EPI_ISL_84900 A H3N2 1972 GISAID 30 | A/Bilthoven/21801/1971 EPI_ISL_113037 A H3N2 1971 GISAID 31 | A/Bilthoven/2271/1976 AY661007 A H3N2 1976 IRD 32 | A/Bilthoven/23290/1972 EPI_ISL_113847 A H3N2 1972 GISAID 33 | A/Bilthoven/23337/1972 EPI_ISL_110819 A H3N2 1972 GISAID 34 | A/Bilthoven/2600/1975 EPI_ISL_113966 A H3N2 1975 GISAID 35 | A/Bilthoven/2668/1970 EPI_ISL_110777 A H3N2 1970 GISAID 36 | A/Bilthoven/2813/1975 EPI_ISL_113967 A H3N2 1975 GISAID 37 | A/Bilthoven/334/1975 EPI_ISL_113921 A H3N2 1975 GISAID 38 | A/Bilthoven/3517/1973 EPI_ISL_113915 A H3N2 1973 GISAID 39 | A/Bilthoven/3895/1977 EPI_ISL_114018 A H3N2 1977 GISAID 40 | A/Bilthoven/4273/1975 EPI_ISL_110822 A H3N2 1975 GISAID 41 | A/Bilthoven/4791/1981 EPI_ISL_110862 A H3N2 1981 GISAID 42 | A/Bilthoven/5029/1976 EPI_ISL_114014 A H3N2 1976 GISAID 43 | A/Bilthoven/5146/1974 CY112329 A H3N2 1974 IRD 44 | A/Bilthoven/5168/1976 CY116575 A H3N2 1976 IRD 45 | A/Bilthoven/552/1973 EPI_ISL_113864 A H3N2 1973 GISAID 46 | A/Bilthoven/5657/1976 EPI_ISL_114015 A H3N2 1976 GISAID 47 | A/Bilthoven/5930/1974 EPI_ISL_113917 A H3N2 1974 GISAID 48 | A/Bilthoven/5931/1974 EPI_ISL_113918 A H3N2 1974 GISAID 49 | A/Bilthoven/6022/1972 EPI_ISL_110780 A H3N2 1972 GISAID 50 | A/Bilthoven/6449/1971 EPI_ISL_110778 A H3N2 1971 GISAID 51 | A/Bilthoven/6545/1976 EPI_ISL_114016 A H3N2 1976 GISAID 52 | A/Bilthoven/7398/1974 EPI_ISL_113919 A H3N2 1974 GISAID 53 | A/Bilthoven/748/1973 EPI_ISL_110820 A H3N2 1973 GISAID 54 | A/Bilthoven/808/1969 EPI_ISL_110747 A H3N2 1969 GISAID 55 | A/Bilthoven/908/1969 EPI_ISL_113017 A H3N2 1969 GISAID 56 | A/Bilthoven/93/1970 CY112265 A H3N2 1970 IRD 57 | A/Bilthoven/9459/1974 EPI_ISL_113920 A H3N2 1974 GISAID 58 | A/Bratislava/31/2011 EPI_ISL_99869 A H3N2 2011 GISAID 59 | A/Brazil/1742/2005 EPI_ISL_17364 A H3N2 2005 GISAID 60 | A/Brisbane/10/2007 EPI_ISL_110723 A H3N2 2007 GISAID 61 | A/Brisbane/11/2010 EPI_ISL_78688 A H3N2 2010 GISAID 62 | A/Brisbane/24/2008 EPI_ISL_23848 A H3N2 2008 GISAID 63 | A/Brisbane/3/2005 EF566225 A H3N2 2005 IRD 64 | A/Brisbane/5/2002 EU501129 A H3N2 2002 IRD 65 | A/Brisbane/6/2002 EU501130 A H3N2 2002 IRD 66 | A/Brisbane/7/2003 EU501209 A H3N2 2003 IRD 67 | A/Brisbane/8/1996 EPI_ISL_115771 A H3N2 1996 GISAID 68 | A/Brisbane/9/2006 CY121568 A H3N2 2006 IRD 69 | A/Caen/1/1984 EPI_ISL_901 A H3N2 1984 GISAID 70 | A/California/20/2005 EF473440 A H3N2 2005 IRD 71 | A/California/7/2004 EPI_ISL_113070 A H3N2 2004 GISAID 72 | A/Cameroon/675/2009 EPI_ISL_77111 A H3N2 2009 GISAID 73 | A/Canada/578/2004 EPI_ISL_21872 A H3N2 2004 GISAID 74 | A/Cheonnam/432/2002 AY589653 A H3N2 2002 IRD 75 | A/ChristChurch/2/1988 AF008905 A H3N2 1988 IRD 76 | A/ChristChurch/28/2003 EPI_ISL_11942 A H3N2 2003 GISAID 77 | A/Colorado/2/1986 EPI_ISL_114293 A H3N2 1986 GISAID 78 | A/Daejeon/390/2002 EPI_ISL_3928 A H3N2 2002 GISAID 79 | A/Durban/92/2011 EPI_ISL_96032 A H3N2 2011 GISAID 80 | A/Eindhoven/3447/1989 EPI_ISL_110906 A H3N2 1989 GISAID 81 | A/England/138/1989 EPI_ISL_114346 A H3N2 1989 GISAID 82 | A/England/392/2008 CY088444 A H3N2 2008 IRD 83 | A/England/394/2008 CY088445 A H3N2 2008 IRD 84 | A/England/42/1972 CY121157 A H3N2 1972 IRD 85 | A/England/427/1988 EPI_ISL_114296 A H3N2 1988 GISAID 86 | A/England/669/2008 EPI_ISL_61706 A H3N2 2008 GISAID 87 | A/England/687/2008 EPI_ISL_61707 A H3N2 2008 GISAID 88 | A/England/7/1994 EPI_ISL_111129 A H3N2 1994 GISAID 89 | A/Finland/170/2003 EPI_ISL_115625 A H3N2 2003 GISAID 90 | A/Finland/338/1995 EPI_ISL_115459 A H3N2 1995 GISAID 91 | A/Finland/339/1995 EPI_ISL_115460 A H3N2 1995 GISAID 92 | A/Finland/381/1995 EPI_ISL_115461 A H3N2 1995 GISAID 93 | A/Finland/9/2008 EPI_ISL_60842 A H3N2 2008 GISAID 94 | A/Florida/2/2006 EPI_ISL_75939 A H3N2 2006 GISAID 95 | A/Florida/43/2010 EPI_ISL_87876 A H3N2 2010 GISAID 96 | A/Fujian/411/2002 EPI_ISL_111384 A H3N2 2002 GISAID 97 | A/Fujian/445/2003 CY121448 A H3N2 2003 IRD 98 | A/Fukuoka/15/2002 EPI_ISL_67628 A H3N2 2002 GISAID 99 | A/Geneva/3958/1996 EPI_ISL_115513 A H3N2 1996 GISAID 100 | A/Geneva/5007/1989 EPI_ISL_110907 A H3N2 1989 GISAID 101 | A/Geneva/AI9509/1995 AY661182 A H3N2 1995 IRD 102 | A/Guadeloupe/202/2010 EPI_ISL_88048 A H3N2 2010 GISAID 103 | A/Guam/228/2002 EPI_ISL_18392 A H3N2 2002 GISAID 104 | A/Guangdong/25/1993 EPI_ISL_115110 A H3N2 1993 GISAID 105 | A/Guildford/V728/1985 EPI_ISL_114246 A H3N2 1985 GISAID 106 | A/Guizhou/54/1989 EPI_ISL_702 A H3N2 1989 GISAID 107 | A/Gunma/16/2005 EPI_ISL_17404 A H3N2 2005 GISAID 108 | A/Hiroshima/39/2004 EPI_ISL_17186 A H3N2 2004 GISAID 109 | A/Hiroshima/52/2005 EPI_ISL_13228 A H3N2 2005 GISAID 110 | A/HongKong/107/1971 EPI_ISL_110779 A H3N2 1971 GISAID 111 | A/HongKong/1/1968 AF348179 A H3N2 1968 IRD 112 | A/HongKong/1/1989 EPI_ISL_110908 A H3N2 1989 GISAID 113 | A/HongKong/1/1994 EPI_ISL_111130 A H3N2 1994 GISAID 114 | A/HongKong/1/1997 EPI_ISL_111271 A H3N2 1997 GISAID 115 | A/HongKong/1550/2002 EU514627 A H3N2 2002 IRD 116 | A/HongKong/1952/2009 EPI_ISL_60839 A H3N2 2009 GISAID 117 | A/HongKong/1985/2009 EPI_ISL_60840 A H3N2 2009 GISAID 118 | A/HongKong/20/1996 EPI_ISL_115514 A H3N2 1996 GISAID 119 | A/HongKong/218/2006 EPI_ISL_22000 A H3N2 2006 GISAID 120 | A/HongKong/2/1994 EPI_ISL_111131 A H3N2 1994 GISAID 121 | A/HongKong/26560/2009 CY121736 A H3N2 2009 IRD 122 | A/HongKong/280/1997 CY112845 A H3N2 1997 IRD 123 | A/HongKong/2831/2005 EPI_ISL_64664 A H3N2 2005 GISAID 124 | A/HongKong/3170/2010 EPI_ISL_81380 A H3N2 2010 GISAID 125 | A/HongKong/3/1995 EPI_ISL_115463 A H3N2 1995 GISAID 126 | A/HongKong/32/1995 CY112765 A H3N2 1995 IRD 127 | A/HongKong/34430/2009 EPI_ISL_66704 A H3N2 2009 GISAID 128 | A/HongKong/357/1996 EPI_ISL_115563 A H3N2 1996 GISAID 129 | A/HongKong/358/1996 EPI_ISL_115564 A H3N2 1996 GISAID 130 | A/HongKong/38/1995 CY112773 A H3N2 1995 IRD 131 | A/HongKong/3969/2011 EPI_ISL_94725 A H3N2 2011 GISAID 132 | A/HongKong/42/1996 EPI_ISL_115515 A H3N2 1996 GISAID 133 | A/HongKong/434/1996 EPI_ISL_115565 A H3N2 1996 GISAID 134 | A/HongKong/49/1995 EPI_ISL_115510 A H3N2 1995 GISAID 135 | A/HongKong/55/1994 CY112725 A H3N2 1994 IRD 136 | A/HongKong/55/1995 EPI_ISL_111173 A H3N2 1995 GISAID 137 | A/HongKong/56/1994 EPI_ISL_115414 A H3N2 1994 GISAID 138 | A/HongKong/734/2001 EPI_ISL_100391 A H3N2 2001 GISAID 139 | A/Idaho/2008/2003 EPI_ISL_17946 A H3N2 2003 GISAID 140 | A/Incheon/677/2006 EPI_ISL_20293 A H3N2 2006 GISAID 141 | A/Iowa/19/2010 EPI_ISL_88046 A H3N2 2010 GISAID 142 | A/Ishikawa/102/2002 EPI_ISL_11491 A H3N2 2002 GISAID 143 | A/Israel/22/2009 EPI_ISL_77134 A H3N2 2009 GISAID 144 | A/Israel/24/2009 EPI_ISL_77132 A H3N2 2009 GISAID 145 | A/Israel/26/2009 EPI_ISL_77133 A H3N2 2009 GISAID 146 | A/Johannesburg/10/1997 EPI_ISL_111314 A H3N2 1997 GISAID 147 | A/Johannesburg/107/2011 EPI_ISL_96037 A H3N2 2011 GISAID 148 | A/Johannesburg/113/2011 EPI_ISL_96036 A H3N2 2011 GISAID 149 | A/Johannesburg/114/2011 EPI_ISL_96038 A H3N2 2011 GISAID 150 | A/Johannesburg/15/2008 EPI_ISL_60841 A H3N2 2008 GISAID 151 | A/Johannesburg/153/2011 EPI_ISL_96035 A H3N2 2011 GISAID 152 | A/Johannesburg/33/1994 CY112733 A H3N2 1994 IRD 153 | A/Johannesburg/47/1994 CY112741 A H3N2 1994 IRD 154 | A/Johannesburg/73/2011 EPI_ISL_96029 A H3N2 2011 GISAID 155 | A/Johannesburg/78/2011 EPI_ISL_96030 A H3N2 2011 GISAID 156 | A/Johannesburg/79/2011 EPI_ISL_96031 A H3N2 2011 GISAID 157 | A/Johannesburg/94/2011 EPI_ISL_96033 A H3N2 2011 GISAID 158 | A/Johannesburg/99/2011 EPI_ISL_96034 A H3N2 2011 GISAID 159 | A/Kentucky/3/2006 EPI_ISL_21271 A H3N2 2006 GISAID 160 | A/Kitakyushu/5/2006 EPI_ISL_17705 A H3N2 2006 GISAID 161 | A/Korea/770/2002 EPI_ISL_11661 A H3N2 2002 GISAID 162 | A/Kumamoto/102/2002 EPI_ISL_11445 A H3N2 2002 GISAID 163 | A/Leningrad/360/1986 CY121277 A H3N2 1986 IRD 164 | A/Louisiana/4/2003 EF473536 A H3N2 2003 IRD 165 | A/Lyon/108/2005 EF566232 A H3N2 2005 IRD 166 | A/Lyon/1149/1991 EPI_ISL_114504 A H3N2 1991 GISAID 167 | A/Lyon/1182/1991 EPI_ISL_114505 A H3N2 1991 GISAID 168 | A/Lyon/1292/2006 EPI_ISL_20282 A H3N2 2006 GISAID 169 | A/Lyon/1313/2006 EPI_ISL_20284 A H3N2 2006 GISAID 170 | A/Lyon/1324/2006 EPI_ISL_20286 A H3N2 2006 GISAID 171 | A/Lyon/1331/2006 EPI_ISL_20288 A H3N2 2006 GISAID 172 | A/Lyon/1359/2006 EPI_ISL_20289 A H3N2 2006 GISAID 173 | A/Lyon/1381/2007 EPI_ISL_19157 A H3N2 2007 GISAID 174 | A/Lyon/1781/1996 EPI_ISL_115566 A H3N2 1996 GISAID 175 | A/Lyon/2279/1995 EPI_ISL_115511 A H3N2 1995 GISAID 176 | A/Lyon/2380/1981 EPI_ISL_114199 A H3N2 1981 GISAID 177 | A/Lyon/24222/1991 EPI_ISL_114559 A H3N2 1991 GISAID 178 | A/Lyon/636/2006 EPI_ISL_64166 A H3N2 2006 GISAID 179 | A/Lyon/672/1993 EPI_ISL_115111 A H3N2 1993 GISAID 180 | A/Lyon/Cx-R/3120/2009 EPI_ISL_77121 A H3N2 2009 GISAID 181 | A/Madrid/G102/1993 EPI_ISL_111020 A H3N2 1993 GISAID 182 | A/Madrid/G109/1993 EPI_ISL_115302 A H3N2 1993 GISAID 183 | A/Madrid/G12/1991 EPI_ISL_114607 A H3N2 1991 GISAID 184 | A/Madrid/G122/1993 EPI_ISL_115300 A H3N2 1993 GISAID 185 | A/Madrid/G130/1993 CY112573 A H3N2 1993 IRD 186 | A/Madrid/G252/1993 EPI_ISL_115304 A H3N2 1993 GISAID 187 | A/Madrid/G58/1992 EPI_ISL_114657 A H3N2 1992 GISAID 188 | A/Malaysia/1/2004 EPI_ISL_11955 A H3N2 2004 GISAID 189 | A/Memphis/2/1990 EPI_ISL_114452 A H3N2 1990 GISAID 190 | A/Memphis/5/1990 EPI_ISL_114453 A H3N2 1990 GISAID 191 | A/Minnesota/17/2010 EPI_ISL_87923 A H3N2 2010 GISAID 192 | A/Mississippi/1/1985 EPI_ISL_68905 A H3N2 1985 GISAID 193 | A/Mississippi/5/2004 EPI_ISL_21236 A H3N2 2004 GISAID 194 | A/Montana/439520/2005 EPI_ISL_64714 A H3N2 2005 GISAID 195 | A/Montana/5/2011 EPI_ISL_89798 A H3N2 2011 GISAID 196 | A/Moscow/10/1999 EPI_ISL_2695 A H3N2 1999 GISAID 197 | A/Nanchang/933/1995 EPI_ISL_111174 A H3N2 1995 GISAID 198 | A/Nepal/1646/2004 EPI_ISL_17243 A H3N2 2004 GISAID 199 | A/Nepal/921/2006 CY121512 A H3N2 2006 IRD 200 | A/Netherlands/101/1993 EPI_ISL_115305 A H3N2 1993 GISAID 201 | A/Netherlands/115/1993 CY112597 A H3N2 1993 IRD 202 | A/Netherlands/118/2001 EPI_ISL_111376 A H3N2 2001 GISAID 203 | A/Netherlands/1/1995 EPI_ISL_115512 A H3N2 1995 GISAID 204 | A/Netherlands/1/2002 EPI_ISL_110654 A H3N2 2002 GISAID 205 | A/Netherlands/124/2001 EPI_ISL_115622 A H3N2 2001 GISAID 206 | A/Netherlands/126/1993 EPI_ISL_115353 A H3N2 1993 GISAID 207 | A/Netherlands/126/2001 EPI_ISL_115623 A H3N2 2001 GISAID 208 | A/Netherlands/18/1994 EPI_ISL_115458 A H3N2 1994 GISAID 209 | A/Netherlands/209/1980 EPI_ISL_114198 A H3N2 1980 GISAID 210 | A/Netherlands/22/2003 EPI_ISL_110690 A H3N2 2003 GISAID 211 | A/Netherlands/241/1982 EPI_ISL_114201 A H3N2 1982 GISAID 212 | A/Netherlands/241/1993 EPI_ISL_111044 A H3N2 1993 GISAID 213 | A/Netherlands/271/1995 EPI_ISL_111181 A H3N2 1995 GISAID 214 | A/Netherlands/300/1997 EPI_ISL_115619 A H3N2 1997 GISAID 215 | A/Netherlands/301/1999 EPI_ISL_84904 A H3N2 1999 GISAID 216 | A/Netherlands/3/1993 EPI_ISL_111022 A H3N2 1992 GISAID 217 | A/Netherlands/3/2000 EPI_ISL_115621 A H3N2 2000 GISAID 218 | A/Netherlands/330/1985 EPI_ISL_114247 A H3N2 1985 GISAID 219 | A/Netherlands/333/1985 EPI_ISL_114248 A H3N2 1985 GISAID 220 | A/Netherlands/371/1993 CY112621 A H3N2 1993 IRD 221 | A/Netherlands/414/1998 CY112893 A H3N2 1998 IRD 222 | A/Netherlands/427/1998 EPI_ISL_111373 A H3N2 1998 GISAID 223 | A/Netherlands/450/1988 EPI_ISL_114297 A H3N2 1988 GISAID 224 | A/Netherlands/462/1998 EPI_ISL_115620 A H3N2 1998 GISAID 225 | A/Netherlands/5/1998 EPI_ISL_115772 A H3N2 1998 GISAID 226 | A/Netherlands/620/1989 EPI_ISL_114347 A H3N2 1989 GISAID 227 | A/Netherlands/650/1989 EPI_ISL_114348 A H3N2 1989 GISAID 228 | A/Netherlands/738/1989 EPI_ISL_114349 A H3N2 1989 GISAID 229 | A/Netherlands/816/1991 EPI_ISL_114608 A H3N2 1991 GISAID 230 | A/Netherlands/823/1992 EPI_ISL_114661 A H3N2 1992 GISAID 231 | A/Netherlands/891/1991 EPI_ISL_114609 A H3N2 1991 GISAID 232 | A/Netherlands/91/1996 EPI_ISL_115567 A H3N2 1996 GISAID 233 | A/Netherlands/935/1992 EPI_ISL_114659 A H3N2 1992 GISAID 234 | A/Netherlands/938/1992 EPI_ISL_114660 A H3N2 1991 GISAID 235 | A/Nevada/5/2007 EPI_ISL_15411 A H3N2 2007 GISAID 236 | A/NewCaledonia/20/2003 EPI_ISL_67242 A H3N2 2003 GISAID 237 | A/NewCaledonia/6/2002 EU501162 A H3N2 2002 IRD 238 | A/NewYork/55/2004 EPI_ISL_22628 A H3N2 2004 GISAID 239 | A/Nice/491/1997 EPI_ISL_111339 A H3N2 1996 GISAID 240 | A/Nijmegen/3126/1992 EPI_ISL_114705 A H3N2 1992 GISAID 241 | A/Nijmegen/3129/1992 EPI_ISL_114706 A H3N2 1992 GISAID 242 | A/NordrheinWestfalen/1/2010 EPI_ISL_77118 A H3N2 2010 GISAID 243 | A/NorthCarolina/13/2005 EPI_ISL_11608 A H3N2 2005 GISAID 244 | A/NorthDakota/1/2004 EPI_ISL_21241 A H3N2 2004 GISAID 245 | A/Norway/1/2009 EPI_ISL_61756 A H3N2 2008 GISAID 246 | A/Norway/1762/2011 EPI_ISL_95094 A H3N2 2011 GISAID 247 | A/Norway/1775/2011 EPI_ISL_95095 A H3N2 2011 GISAID 248 | A/Norway/3789/2009 EPI_ISL_77128 A H3N2 2009 GISAID 249 | A/Norway/3790/2009 EPI_ISL_77129 A H3N2 2009 GISAID 250 | A/Okayama/29/2005 EPI_ISL_17495 A H3N2 2005 GISAID 251 | A/Oklahoma/5/1988 EPI_ISL_115768 A H3N2 1988 GISAID 252 | A/Oklahoma/8/2004 EPI_ISL_67261 A H3N2 2003 GISAID 253 | A/Osaka/56/2004 EPI_ISL_65565 A H3N2 2004 GISAID 254 | A/Oslo/13676/1983 EPI_ISL_114245 A H3N2 1983 GISAID 255 | A/Oslo/21/1997 EPI_ISL_111315 A H3N2 1997 GISAID 256 | A/Oslo/2352/1993 CY112877 A H3N2 1993 IRD 257 | A/Oslo/244/1997 CY112645 A H3N2 1997 IRD 258 | A/Oviedo/31/1992 EPI_ISL_114707 A H3N2 1991 GISAID 259 | A/Panama/2007/1999 EPI_ISL_2674 A H3N2 1999 GISAID 260 | A/Paris/207/2002 EPI_ISL_67668 A H3N2 2002 GISAID 261 | A/Paris/320/1992 EPI_ISL_114708 A H3N2 1991 GISAID 262 | A/Paris/325/1992 EPI_ISL_114709 A H3N2 1991 GISAID 263 | A/Paris/407/1992 EPI_ISL_114710 A H3N2 1991 GISAID 264 | A/Paris/424/1992 EPI_ISL_114759 A H3N2 1991 GISAID 265 | A/Paris/457/1992 EPI_ISL_114760 A H3N2 1991 GISAID 266 | A/Paris/458/2008 EPI_ISL_61719 A H3N2 2008 GISAID 267 | A/Paris/467/1992 EPI_ISL_114761 A H3N2 1991 GISAID 268 | A/Paris/490/1992 EPI_ISL_4296 A H3N2 1992 GISAID 269 | A/Paris/512/1992 EPI_ISL_114762 A H3N2 1991 GISAID 270 | A/Paris/548/1992 EPI_ISL_114763 A H3N2 1991 GISAID 271 | A/Paris/564/1992 EPI_ISL_114811 A H3N2 1991 GISAID 272 | A/Paris/583/1992 EPI_ISL_114812 A H3N2 1992 GISAID 273 | A/Paris/597/1992 EPI_ISL_114813 A H3N2 1991 GISAID 274 | A/Paris/614/1992 EPI_ISL_114814 A H3N2 1992 GISAID 275 | A/Perth/10/2010 EPI_ISL_78687 A H3N2 2010 GISAID 276 | A/Perth/16/2009 EPI_ISL_31055 A H3N2 2009 GISAID 277 | A/Peru/1296/2004 EPI_ISL_17285 A H3N2 2004 GISAID 278 | A/Philippines/1159050/2002 EU514667 A H3N2 2002 IRD 279 | A/Philippines/2191/2009 EPI_ISL_66607 A H3N2 2009 GISAID 280 | A/Philippines/2/1982 EPI_ISL_76487 A H3N2 1982 GISAID 281 | A/Philippines/472/2002 EPI_ISL_16949 A H3N2 2002 GISAID 282 | A/Philippines/825/2003 EPI_ISL_11977 A H3N2 2003 GISAID 283 | A/Poitiers/1341/2008 EPI_ISL_61723 A H3N2 2008 GISAID 284 | A/PortChalmers/1/1973 EPI_ISL_113916 A H3N2 1973 GISAID 285 | A/Pusan/504/2002 EPI_ISL_3919 A H3N2 2002 GISAID 286 | A/RhodeIsland/1/2010 CY121800 A H3N2 2010 IRD 287 | A/Romania/802-03/2003 EPI_ISL_18064 A H3N2 2003 GISAID 288 | A/Rotterdam/577/1980 EPI_ISL_110861 A H3N2 1980 GISAID 289 | A/Rotterdam/5828/1977 EPI_ISL_114019 A H3N2 1977 GISAID 290 | A/Rotterdam/8179/1977 EPI_ISL_114196 A H3N2 1977 GISAID 291 | A/Sakai/20/2011 EPI_ISL_93012 A H3N2 2011 GISAID 292 | A/Sendai/C273/1992 EPI_ISL_110995 A H3N2 1992 GISAID 293 | A/Seoul/1/1990 AY661072 A H3N2 1990 IRD 294 | A/Seoul/4436/2008 EPI_ISL_61735 A H3N2 2008 GISAID 295 | A/Serres/77/2007 EPI_ISL_20632 A H3N2 2007 GISAID 296 | A/Shandong/9/1993 EPI_ISL_115410 A H3N2 1993 GISAID 297 | A/Shanghai/11/1987 EPI_ISL_114294 A H3N2 1987 GISAID 298 | A/Shanghai/24/1990 EPI_ISL_114454 A H3N2 1990 GISAID 299 | A/Shanghai/369/2003 EPI_ISL_67277 A H3N2 2003 GISAID 300 | A/Shiga/6/1993 CY112653 A H3N2 1993 IRD 301 | A/Sichuan/2/1987 EPI_ISL_110865 A H3N2 1987 GISAID 302 | A/Singapore/1/1996 EPI_ISL_111270 A H3N2 1996 GISAID 303 | A/Singapore/15/2001 EPI_ISL_100404 A H3N2 2001 GISAID 304 | A/Singapore/34/1989 EPI_ISL_114396 A H3N2 1989 GISAID 305 | A/Singapore/35/1989 EPI_ISL_114397 A H3N2 1989 GISAID 306 | A/Singapore/35/2005 EU501773 A H3N2 2005 IRD 307 | A/Singapore/36/1989 EPI_ISL_115411 A H3N2 1989 GISAID 308 | A/Singapore/36/2004 EPI_ISL_21116 A H3N2 2004 GISAID 309 | A/Singapore/37/2004 EPI_ISL_12068 A H3N2 2004 GISAID 310 | A/Singapore/38/2005 EU501774 A H3N2 2005 IRD 311 | A/Singapore/40/1989 EPI_ISL_114398 A H3N2 1989 GISAID 312 | A/Singapore/53/1989 EPI_ISL_110909 A H3N2 1989 GISAID 313 | A/Singapore/57/2006 EU502049 A H3N2 2006 IRD 314 | A/Singapore/70/2005 DQ865951 A H3N2 2005 IRD 315 | A/Singapore/95/2003 EU501320 A H3N2 2003 IRD 316 | A/Singapore/N593/2008 EPI_ISL_61726 A H3N2 2008 GISAID 317 | A/Sofia/141/2003 EU501322 A H3N2 2003 IRD 318 | A/Sofia/319/2007 EPI_ISL_20633 A H3N2 2007 GISAID 319 | A/SouthAustralia/102/2001 EU501121 A H3N2 2001 IRD 320 | A/SouthAustralia/15/1994 EPI_ISL_111135 A H3N2 1994 GISAID 321 | A/SouthAustralia/23/1992 AY661127 A H3N2 1992 IRD 322 | A/SouthAustralia/25/1994 EPI_ISL_111170 A H3N2 1994 GISAID 323 | A/SouthAustralia/27/1992 AY661128 A H3N2 1992 IRD 324 | A/SouthAustralia/3/2011 EPI_ISL_95227 A H3N2 2011 GISAID 325 | A/SouthAustralia/8/1992 EPI_ISL_110996 A H3N2 1992 GISAID 326 | A/Stockholm/10/1985 EPI_ISL_114249 A H3N2 1985 GISAID 327 | A/Stockholm/112/2009 EPI_ISL_68574 A H3N2 2009 GISAID 328 | A/Stockholm/1/2010 EPI_ISL_81390 A H3N2 2010 GISAID 329 | A/Stockholm/12/1988 EPI_ISL_114298 A H3N2 1988 GISAID 330 | A/Stockholm/12/1992 EPI_ISL_114868 A H3N2 1992 GISAID 331 | A/Stockholm/13/1992 EPI_ISL_114869 A H3N2 1992 GISAID 332 | A/Stockholm/18/2011 EPI_ISL_90426 A H3N2 2011 GISAID 333 | A/Stockholm/20/1991 EPI_ISL_110951 A H3N2 1991 GISAID 334 | A/Stockholm/20/1993 EPI_ISL_111081 A H3N2 1993 GISAID 335 | A/Stockholm/2/2010 EPI_ISL_81391 A H3N2 2010 GISAID 336 | A/Stockholm/26/2008 EPI_ISL_70811 A H3N2 2008 GISAID 337 | A/Stockholm/7/1992 EPI_ISL_114867 A H3N2 1992 GISAID 338 | A/Stockholm/8/1992 EPI_ISL_110997 A H3N2 1992 GISAID 339 | A/Stockholm/89/2009 EPI_ISL_68567 A H3N2 2009 GISAID 340 | A/Sweden/2/2009 EPI_ISL_68566 A H3N2 2009 GISAID 341 | A/Sweden/3/2008 EPI_ISL_70653 A H3N2 2008 GISAID 342 | A/Switzerland/1397477/2008 EPI_ISL_61731 A H3N2 2008 GISAID 343 | A/Switzerland/1409281/2008 EPI_ISL_61732 A H3N2 2008 GISAID 344 | A/Sydney/5/1997 EPI_ISL_111337 A H3N2 1997 GISAID 345 | A/Taiwan/1529/2003 EPI_ISL_17108 A H3N2 2003 GISAID 346 | A/Taiwan/51/2005 EPI_ISL_10419 A H3N2 2005 GISAID 347 | A/Taiwan/760/2007 EPI_ISL_22363 A H3N2 2007 GISAID 348 | A/Taiwan/8/2002 EPI_ISL_16964 A H3N2 2002 GISAID 349 | A/Taiwan/83/2006 EU124073 A H3N2 2006 IRD 350 | A/Taiwan/99/2006 EPI_ISL_17795 A H3N2 2006 GISAID 351 | A/Tanger/533/2009 EPI_ISL_61768 A H3N2 2008 GISAID 352 | A/Tennessee/6/2004 EPI_ISL_11815 A H3N2 2004 GISAID 353 | A/Texas/1/1977 EPI_ISL_114197 A H3N2 1977 GISAID 354 | A/Texas/37/2007 EPI_ISL_21289 A H3N2 2007 GISAID 355 | A/Texas/40/2003 EF473582 A H3N2 2003 IRD 356 | A/Texas/6/2004 EPI_ISL_11817 A H3N2 2004 GISAID 357 | A/Tilburg/5957/1992 EPI_ISL_114870 A H3N2 1991 GISAID 358 | A/Torino/14/2008 EPI_ISL_61751 A H3N2 2008 GISAID 359 | A/Toulon/1244/2006 EPI_ISL_20276 A H3N2 2006 GISAID 360 | A/Toulouse/878/2001 EPI_ISL_121223 A H3N2 2001 GISAID 361 | A/Townsville/1/2003 EPI_ISL_67296 A H3N2 2003 GISAID 362 | A/Trieste/25c/2007 EPI_ISL_98951 A H3N2 2007 GISAID 363 | A/Ukraine/13/2006 EPI_ISL_17812 A H3N2 2006 GISAID 364 | A/Ulaanbaatar/3849/2010 EPI_ISL_87879 A H3N2 2010 GISAID 365 | A/Umea/2000/1992 EPI_ISL_114872 A H3N2 1992 GISAID 366 | A/Umea/4/2009 EPI_ISL_68571 A H3N2 2009 GISAID 367 | A/Uppsala/3/2011 EPI_ISL_90058 A H3N2 2011 GISAID 368 | A/Uruguay/716/2007 CY121632 A H3N2 2007 IRD 369 | A/Uvurkhangai/3970/2010 EPI_ISL_87878 A H3N2 2010 GISAID 370 | A/Victoria/102/2003 EU501345 A H3N2 2002 IRD 371 | A/Victoria/110/2004 EPI_ISL_21139 A H3N2 2004 GISAID 372 | A/Victoria/1/1988 EPI_ISL_115700 A H3N2 1988 GISAID 373 | A/Victoria/1/1989 EPI_ISL_114399 A H3N2 1989 GISAID 374 | A/Victoria/208/2009 EPI_ISL_33598 A H3N2 2009 GISAID 375 | A/Victoria/210/2009 EPI_ISL_33814 A H3N2 2009 GISAID 376 | A/Victoria/2/1990 EPI_ISL_114456 A H3N2 1990 GISAID 377 | A/Victoria/3/1975 V01098 A H3N2 1975 IRD 378 | A/Victoria/33/1992 EPI_ISL_110998 A H3N2 1992 GISAID 379 | A/Victoria/500/2004 EPI_ISL_12069 A H3N2 2004 GISAID 380 | A/Victoria/503/2006 EPI_ISL_13265 A H3N2 2006 GISAID 381 | A/Victoria/523/2004 EPI_ISL_12064 A H3N2 2004 GISAID 382 | A/Victoria/7/1987 AF008888 A H3N2 1987 IRD 383 | A/Victoria/75/1995 EPI_ISL_111220 A H3N2 1995 GISAID 384 | A/Waikato/1/1989 EPI_ISL_114401 A H3N2 1989 GISAID 385 | A/Washington/1/2004 EPI_ISL_11522 A H3N2 2004 GISAID 386 | A/Wellington/1/2004 CY121480 A H3N2 2004 IRD 387 | A/Wellington/3/1990 EPI_ISL_114457 A H3N2 1990 GISAID 388 | A/Wellington/4/1985 EPI_ISL_114250 A H3N2 1985 GISAID 389 | A/Wellington/5/1989 EPI_ISL_114400 A H3N2 1989 GISAID 390 | A/Wisconsin/13/2010 EPI_ISL_86092 A H3N2 2010 GISAID 391 | A/Wisconsin/15/2009 CY121041 A H3N2 2009 IRD 392 | A/Wisconsin/19/2004 EPI_ISL_21255 A H3N2 2004 GISAID 393 | A/Wisconsin/3/2007 CY121528 A H3N2 2007 IRD 394 | A/Wisconsin/67/2005 EPI_ISL_115646 A H3N2 2005 GISAID 395 | A/Wisconsin/68/2005 EPI_ISL_17572 A H3N2 2005 GISAID 396 | A/Wuhan/359/1995 CY112821 A H3N2 1995 IRD 397 | A/Wyoming/0049/2005 EPI_ISL_18160 A H3N2 2005 GISAID 398 | A/Wyoming/1/2006 EPI_ISL_17823 A H3N2 2006 GISAID 399 | A/Wyoming/2/2003 EF473602 A H3N2 2003 IRD 400 | A/Wyoming/3/2003 EPI_ISL_3767 A H3N2 2003 GISAID 401 | A/Yamagata/56/1993 EPI_ISL_115412 A H3N2 1993 GISAID 402 | A/Yamagata/61/1993 EPI_ISL_115413 A H3N2 1993 GISAID 403 | A/Yamagata/62/1993 CY112693 A H3N2 1993 IRD 404 | -------------------------------------------------------------------------------- /example-xmls/H1N1_mds_drift_effects_tree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 1.0 1.0 8 | 9 | 10 | 11 | 1.0 1.0 12 | 13 | 14 | 15 | 1.0 1.0 16 | 17 | 18 | 19 | 1.0 1.0 20 | 21 | 22 | 23 | 1.0 1.0 24 | 25 | 26 | 27 | 1.0 1.0 28 | 29 | 30 | 31 | 1.0 1.0 32 | 33 | 34 | 35 | 1.0 1.0 36 | 37 | 38 | 39 | 1.0 1.0 40 | 41 | 42 | 43 | 1.0 1.0 44 | 45 | 46 | 47 | 1.0 1.0 48 | 49 | 50 | 51 | 1.0 1.0 52 | 53 | 54 | 55 | 1.0 1.0 56 | 57 | 58 | 59 | 1.0 1.0 60 | 61 | 62 | 63 | 1.0 1.0 64 | 65 | 66 | 67 | 1.0 1.0 68 | 69 | 70 | 71 | 1.0 1.0 72 | 73 | 74 | 75 | 1.0 1.0 76 | 77 | 78 | 79 | 1.0 1.0 80 | 81 | 82 | 83 | 1.0 1.0 84 | 85 | 86 | 87 | 1.0 1.0 88 | 89 | 90 | 91 | 1.0 1.0 92 | 93 | 94 | 95 | 1.0 1.0 96 | 97 | 98 | 99 | 1.0 1.0 100 | 101 | 102 | 103 | 1.0 1.0 104 | 105 | 106 | 107 | 1.0 1.0 108 | 109 | 110 | 111 | 1.0 1.0 112 | 113 | 114 | 115 | 1.0 1.0 116 | 117 | 118 | 119 | 1.0 1.0 120 | 121 | 122 | 123 | 1.0 1.0 124 | 125 | 126 | 127 | 1.0 1.0 128 | 129 | 130 | 131 | 1.0 1.0 132 | 133 | 134 | 135 | 1.0 1.0 136 | 137 | 138 | 139 | 1.0 1.0 140 | 141 | 142 | 143 | 1.0 1.0 144 | 145 | 146 | 147 | 1.0 1.0 148 | 149 | 150 | 151 | 1.0 1.0 152 | 153 | 154 | 155 | 1.0 1.0 156 | 157 | 158 | 159 | 1.0 1.0 160 | 161 | 162 | 163 | 1.0 1.0 164 | 165 | 166 | 167 | 1.0 1.0 168 | 169 | 170 | 171 | 1.0 1.0 172 | 173 | 174 | 175 | 1.0 1.0 176 | 177 | 178 | 179 | 1.0 1.0 180 | 181 | 182 | 183 | 1.0 1.0 184 | 185 | 186 | 187 | 1.0 1.0 188 | 189 | 190 | 191 | 1.0 1.0 192 | 193 | 194 | 195 | 1.0 1.0 196 | 197 | 198 | 199 | 1.0 1.0 200 | 201 | 202 | 203 | 1.0 1.0 204 | 205 | 206 | 207 | 1.0 1.0 208 | 209 | 210 | 211 | 1.0 1.0 212 | 213 | 214 | 215 | 1.0 1.0 216 | 217 | 218 | 219 | 1.0 1.0 220 | 221 | 222 | 223 | 1.0 1.0 224 | 225 | 226 | 227 | 1.0 1.0 228 | 229 | 230 | 231 | 1.0 1.0 232 | 233 | 234 | 235 | 1.0 1.0 236 | 237 | 238 | 239 | 1.0 1.0 240 | 241 | 242 | 243 | 1.0 1.0 244 | 245 | 246 | 247 | 1.0 1.0 248 | 249 | 250 | 251 | 1.0 1.0 252 | 253 | 254 | 255 | 1.0 1.0 256 | 257 | 258 | 259 | 1.0 1.0 260 | 261 | 262 | 263 | 1.0 1.0 264 | 265 | 266 | 267 | 1.0 1.0 268 | 269 | 270 | 271 | 1.0 1.0 272 | 273 | 274 | 275 | 1.0 1.0 276 | 277 | 278 | 279 | 1.0 1.0 280 | 281 | 282 | 283 | 1.0 1.0 284 | 285 | 286 | 287 | 1.0 1.0 288 | 289 | 290 | 291 | 1.0 1.0 292 | 293 | 294 | 295 | 1.0 1.0 296 | 297 | 298 | 299 | 1.0 1.0 300 | 301 | 302 | 303 | 1.0 1.0 304 | 305 | 306 | 307 | 1.0 1.0 308 | 309 | 310 | 311 | 1.0 1.0 312 | 313 | 314 | 315 | 1.0 1.0 316 | 317 | 318 | 319 | 1.0 1.0 320 | 321 | 322 | 323 | 1.0 1.0 324 | 325 | 326 | 327 | 1.0 1.0 328 | 329 | 330 | 331 | 1.0 1.0 332 | 333 | 334 | 335 | 1.0 1.0 336 | 337 | 338 | 339 | 1.0 1.0 340 | 341 | 342 | 343 | 1.0 1.0 344 | 345 | 346 | 347 | 1.0 1.0 348 | 349 | 350 | 351 | 1.0 1.0 352 | 353 | 354 | 355 | 1.0 1.0 356 | 357 | 358 | 359 | 1.0 1.0 360 | 361 | 362 | 363 | 1.0 1.0 364 | 365 | 366 | 367 | 1.0 1.0 368 | 369 | 370 | 371 | 1.0 1.0 372 | 373 | 374 | 375 | 1.0 1.0 376 | 377 | 378 | 379 | 1.0 1.0 380 | 381 | 382 | 383 | 1.0 1.0 384 | 385 | 386 | 387 | 1.0 1.0 388 | 389 | 390 | 391 | 1.0 1.0 392 | 393 | 394 | 395 | 1.0 1.0 396 | 397 | 398 | 399 | 1.0 1.0 400 | 401 | 402 | 403 | 1.0 1.0 404 | 405 | 406 | 407 | 1.0 1.0 408 | 409 | 410 | 411 | 1.0 1.0 412 | 413 | 414 | 415 | 1.0 1.0 416 | 417 | 418 | 419 | 1.0 1.0 420 | 421 | 422 | 423 | 1.0 1.0 424 | 425 | 426 | 427 | 1.0 1.0 428 | 429 | 430 | 431 | 1.0 1.0 432 | 433 | 434 | 435 | 1.0 1.0 436 | 437 | 438 | 439 | 1.0 1.0 440 | 441 | 442 | 443 | 1.0 1.0 444 | 445 | 446 | 447 | 1.0 1.0 448 | 449 | 450 | 451 | 1.0 1.0 452 | 453 | 454 | 455 | 1.0 1.0 456 | 457 | 458 | 459 | 1.0 1.0 460 | 461 | 462 | 463 | 1.0 1.0 464 | 465 | 466 | 467 | 468 | 469 | 470 | 471 | 472 | 473 | 474 | 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 | 484 | 485 | 486 | 487 | 488 | 489 | 490 | 496 | 497 | 498 | 499 | 500 | 501 | 502 | 503 | 504 | 505 | 506 | 507 | 508 | 509 | 510 | 511 | 515 | 516 | 517 | 518 | 519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | 527 | 528 | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 | 542 | 543 | 544 | 545 | 546 | 547 | 548 | 549 | 550 | 551 | 552 | 553 | 554 | 555 | 556 | 557 | 558 | 559 | 560 | 561 | 562 | 563 | 564 | 565 | 566 | 567 | 568 | 569 | 570 | 571 | 572 | 573 | 574 | 575 | 576 | 577 | 578 | 579 | 580 | 581 | 582 | 583 | 584 | 585 | 586 | 587 | 588 | 589 | 590 | 591 | 592 | 593 | 594 | 595 | 596 | 597 | 598 | 599 | 600 | 601 | 602 | 603 | 604 | 605 | 606 | 607 | 608 | 609 | 610 | 611 | 612 | 613 | 614 | 615 | 616 | 617 | 618 | 619 | 620 | 621 | 622 | 623 | 624 | 625 | 626 | 627 | 628 | 629 | 630 | 631 | 632 | 633 | 634 | 635 | 636 | 637 | 638 | 639 | 640 | 641 | 642 | 643 | 644 | 645 | 646 | 647 | 648 | 649 | 650 | 651 | 652 | 653 | 654 | 655 | 656 | 657 | 658 | 659 | 660 | 661 | 662 | 663 | 664 | 665 | 666 | 667 | 668 | 669 | 670 | 671 | 672 | 673 | 674 | 675 | 676 | 677 | 678 | 679 | 680 | 681 | 682 | 683 | 684 | 685 | 686 | 687 | 688 | 689 | 690 | 691 | 692 | 693 | 694 | 695 | 696 | 697 | 698 | 699 | 700 | 701 | 702 | 703 | 704 | 705 | 706 | 707 | 708 | 709 | 710 | 711 | 712 | 713 | 714 | 715 | 716 | 717 | 718 | 719 | 720 | 721 | 722 | 723 | 724 | 725 | 726 | 727 | 728 | 729 | 730 | 731 | 732 | 733 | 734 | 735 | 736 | 737 | 738 | 739 | 740 | 741 | 742 | 743 | 744 | 745 | 746 | 747 | 748 | 749 | 750 | 751 | 752 | 753 | 754 | 755 | 756 | 757 | 758 | 759 | 760 | 761 | 762 | 763 | 764 | 765 | 766 | 767 | 768 | 769 | 770 | 771 | 772 | 773 | 774 | 775 | 776 | 777 | 778 | 779 | 780 | 781 | 782 | 783 | 784 | 785 | 786 | 787 | 788 | 789 | 790 | 791 | 792 | 793 | 794 | --------------------------------------------------------------------------------