├── HomBlocks.pl ├── PartitionFinderV1.1.1 ├── .DS_Store ├── PartitionFinder.py ├── PartitionFinderProtein.py ├── README.md ├── RELEASE-VERSION ├── ROGP_v2.0-backup.pl ├── circoletto.pl ├── docs │ ├── .DS_Store │ └── Manual_v1.1.1.pdf ├── examples │ ├── .DS_Store │ ├── README.txt │ ├── aminoacid │ │ ├── Als_etal_2004.phy │ │ └── partition_finder.cfg │ └── nucleotide │ │ ├── .DS_Store │ │ ├── partition_finder.cfg │ │ └── test.phy ├── partfinder │ ├── .DS_Store │ ├── __init__.py │ ├── __init__.pyc │ ├── algorithm.py │ ├── algorithm.pyc │ ├── alignment.py │ ├── alignment.pyc │ ├── analysis.py │ ├── analysis.pyc │ ├── analysis_method.py │ ├── analysis_method.pyc │ ├── config.py │ ├── config.pyc │ ├── main.py │ ├── main.pyc │ ├── neighbour.py │ ├── neighbour.pyc │ ├── parser.py │ ├── parser.pyc │ ├── partition.py │ ├── partition.pyc │ ├── phyml.py │ ├── phyml.pyc │ ├── phyml_models.py │ ├── phyml_models.pyc │ ├── progress.py │ ├── progress.pyc │ ├── pyparsing.py │ ├── pyparsing.pyc │ ├── raxml.py │ ├── raxml.pyc │ ├── raxml_models.py │ ├── raxml_models.pyc │ ├── reporter.py │ ├── reporter.pyc │ ├── results.py │ ├── results.pyc │ ├── scheme.py │ ├── scheme.pyc │ ├── submodels.py │ ├── submodels.pyc │ ├── subset.py │ ├── subset.pyc │ ├── threadpool.py │ ├── threadpool.pyc │ ├── util.py │ ├── util.pyc │ ├── version.py │ └── version.pyc └── programs │ ├── .DS_Store │ ├── phyml │ └── raxml ├── README.md ├── Xenarthrans └── fasta │ ├── Bradypus_pygmaeus.fasta │ ├── Bradypus_torquatus.fasta │ ├── Bradypus_tridactylus.fasta │ ├── Bradypus_variegatus.fasta │ ├── Bradypus_variegatus_old.fasta │ ├── Cabassous_centralis.fasta │ ├── Cabassous_chacoensis.fasta │ ├── Cabassous_tatouay.fasta │ ├── Cabassous_unicinctus_ISEM_T-2291.fasta │ ├── Cabassous_unicinctus_MNHN_1999-1068.fasta │ ├── Calyptophractus_retusus.fasta │ ├── Chaetophractus_vellerosus.fasta │ ├── Chaetophractus_villosus.fasta │ ├── Chlamyphorus_truncatus.fasta │ ├── Choloepus_didactylus.fasta │ ├── Choloepus_didactylus_old.fasta │ ├── Choloepus_hoffmanni.fasta │ ├── Cyclopes_didactylus.fasta │ ├── Dasypus_hybridus.fasta │ ├── Dasypus_kappleri.fasta │ ├── Dasypus_novemcinctus.fasta │ ├── Dasypus_novemcinctus_old.fasta │ ├── Dasypus_pilosus_LSUMZ_21888.fasta │ ├── Dasypus_pilosus_MSB_49990.fasta │ ├── Dasypus_sabanicola.fasta │ ├── Dasypus_septemcinctus.fasta │ ├── Dasypus_yepesi.fasta │ ├── Euphractus_sexcinctus.fasta │ ├── Myrmecophaga_tridactyla.fasta │ ├── Priodontes_maximus.fasta │ ├── Tamandua_mexicana.fasta │ ├── Tamandua_tetradactyla.fasta │ ├── Tamandua_tetradactyla_old.fasta │ ├── Tolypeutes_matacus.fasta │ ├── Tolypeutes_tricinctus.fasta │ ├── Zaedyus_pichiy.fasta │ └── readme ├── bin ├── BMGE.jar ├── Gblocks ├── blastall ├── formatdb ├── noisy ├── progressiveMauve ├── readal └── trimal └── plant └── fasta ├── Acidosasa_purpurea.fasta ├── Aegilops_cylindrica.fasta ├── Aegilops_geniculata.fasta ├── Aegilops_speltoides_SPE0661.fasta ├── Aegilops_tauschii.fasta ├── Agrostis_stolonifera.fasta ├── Anomochloa_marantoidea.fasta ├── Arundinaria_appalachiana.fasta ├── Arundinaria_gigantea.fasta ├── Arundinaria_tecta.fasta ├── Bambusa_emeiensis.fasta ├── Bambusa_multiplex.fasta ├── Bambusa_oldhamii.fasta ├── Brachypodium_distachyon.fasta ├── Coix_lacryma-jobi.fasta ├── Dendrocalamus_latiflorus.fasta ├── Deschampsia_antarctica.fasta ├── Ferrocalamus_rimosivaginus.fasta ├── Festuca_altissima.fasta ├── Festuca_arundinacea.fasta ├── Festuca_ovina.fasta ├── Festuca_pratensis.fasta ├── Hordeum_vulgare_sub_vulgare.fasta ├── Indocalamus_longiauritus.fasta ├── Leersia_tisserantii.fasta ├── Lolium_multiflorum.fasta ├── Lolium_perenne.fasta ├── Oryza_meridionalis.fasta ├── Oryza_nivara.fasta ├── Oryza_rufipogon.fasta ├── Oryza_sativa_93-11.fasta ├── Oryza_sativa_Nipponbare.fasta ├── Panicum_virgatum.fasta ├── Pharus_lappulaceus.fasta ├── Pharus_latifolius.fasta ├── Phragmites_australis.fasta ├── Phyllostachys_edulis.fasta ├── Phyllostachys_nigra_var_henonis.fasta ├── Phyllostachys_propinqua.fasta ├── Puelia_olyriformis.fasta ├── Rhynchoryza_subulata.fasta ├── Saccharum_officinarum.fasta ├── Secale_cereale.fasta ├── Setaria_italica.fasta ├── Sorghum_bicolor.fasta ├── Sorghum_timorense.fasta ├── Triticum_aestivum.fasta ├── Triticum_monococcum.fasta ├── Triticum_urartu.fasta ├── Typha_latifolia.fasta ├── Zea_mays.fasta ├── Zizania_latifolia.fasta └── readme /HomBlocks.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fenghen360/HomBlocks/HEAD/HomBlocks.pl -------------------------------------------------------------------------------- /PartitionFinderV1.1.1/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fenghen360/HomBlocks/HEAD/PartitionFinderV1.1.1/.DS_Store -------------------------------------------------------------------------------- /PartitionFinderV1.1.1/PartitionFinder.py: 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