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Adding test NEXUS file from TreeBASE.

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commit 8e33a7aa513b7a4a8f94bf9f02c7779e42c8aaf7 1 parent 86a1ce8
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  1. +689 −0 Tests/Nexus/bats.nex
  2. +4 −0 Tests/test_Phylo.py
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689 Tests/Nexus/bats.nex
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+#NEXUS
+
+[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.
+
+
+Generated on February 09, 2013; 19:59 GMT
+
+TreeBASE (cc) 1994-2008
+
+Study reference:
+Agnarsson I., Zambrana-torrelio C.M., Flores saldaña N.P., & May-collado L.M. 2011.
+A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia). PLoS
+Currents: Tree of Life, Version 44.
+
+TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S12003]
+
+BEGIN TAXA;
+ TITLE Taxa;
+ DIMENSIONS NTAX=658;
+ TAXLABELS
+ Acerodon_jubatus
+ Aethalops_alecto
+ Ametrida_centurio
+ Anoura_caudifer
+ Anoura_geoffroyi
+ Antrozous_dubiaquercus
+ Antrozous_pallidus
+ Ardops_nichollsi
+ Ariteus_flavescens
+ Artibeus_amplus
+ Artibeus_anderseni
+ Artibeus_aztecus
+ Artibeus_cf__jamaicensis
+ Artibeus_cf__obscurus
+ Artibeus_cinereus
+ Artibeus_concolor
+ Artibeus_fimbriatus
+ Artibeus_fraterculus
+ Artibeus_fuliginosus
+ Artibeus_glaucus
+ Artibeus_glaucus_bogotensis
+ Artibeus_glaucus_gnomus
+ Artibeus_glaucus_watsoni
+ Artibeus_hartii
+ Artibeus_hirsutus
+ Artibeus_inopinatus
+ Artibeus_intermedius
+ Artibeus_jamaicensis_aequatorialis
+ Artibeus_jamaicensis_jamaicensis
+ Artibeus_jamaicensis_parvipes
+ Artibeus_jamaicensis_paulus
+ Artibeus_jamaicensis_richardsoni
+ Artibeus_jamaicensis_trinitatis
+ Artibeus_jamaicensis_triomylus
+ Artibeus_jamaicensis_yucatanicus
+ Artibeus_lituratus
+ Artibeus_obscurus
+ Artibeus_phaeotis
+ Artibeus_planirostris_fallax
+ Artibeus_planirostris_grenadensis
+ Artibeus_planirostris_hercules
+ Artibeus_planirostris_planirostris
+ Artibeus_planirostris_trinitatis
+ Artibeus_schwartzi
+ Artibeus_sp__FURB
+ Artibeus_toltecus
+ Asellia_tridens
+ Aselliscus_stoliczkanus
+ Aselliscus_tricuspidatus
+ Balantiopteryx_infusca
+ Balantiopteryx_io
+ Balantiopteryx_plicata
+ Balionycteris_maculata
+ Barbastella_barbastellus
+ Barbastella_beijingensis
+ Barbastella_leucomelas
+ Bos_frontalis
+ Brachyphylla_cavernarum
+ Brachyphylla_nana
+ Brachyphylla_pumila
+ Canis_lupus_familiaris
+ Carollia_benkeithi
+ Carollia_brevicauda
+ Carollia_castanea
+ Carollia_sowelli
+ Carollia_subrufa
+ Centronycteris_centralis
+ Centronycteris_maximiliani
+ Centurio_senex
+ Centurio_senex_greenhalli
+ Chaerephon_ansorgei
+ Chaerephon_chapini
+ Chaerephon_jobensis
+ Chaerephon_leucogaster
+ Chaerephon_nigeriae
+ Chaerephon_pumila
+ Chalinolobus_tuberculatus
+ Chilonatalus_micropus
+ Chilonatalus_tumidifrons
+ Chiroderma_doriae
+ Chiroderma_improvisum
+ Chiroderma_salvini
+ Chiroderma_trinitatum
+ Chiroderma_villosum
+ Chironax_melanocephalus
+ Chrotopterus_auritus
+ Chrotopterus_auritus2
+ Cloeotis_percivali
+ Coelops_frithii
+ Cormura_brevirostris
+ Craseonycteris_thonglongyai
+ Cynomops_paranus
+ Cynopterus_brachyotis
+ Cynopterus_horsfieldii
+ Cynopterus_sphinx
+ Cyttarops_alecto
+ Dermanura_bogotensis
+ Dermanura_incomitata
+ Dermanura_rava
+ Dermanura_rosenbergi
+ Desmalopex_leucopterus
+ Desmalopex_microleucopterus
+ Desmodus_rotundus
+ Diaemus_youngi
+ Diclidurus_albus
+ Diclidurus_ingens
+ Diclidurus_isabellus
+ Diclidurus_scutatus
+ Diphylla_ecaudata
+ Dobsonia_inermis
+ Dobsonia_minor
+ Dobsonia_moluccensis
+ Dyacopterus_spadiceus
+ Ectophylla_alba
+ Emballonura_alecto
+ Emballonura_atrata
+ Emballonura_beccarii
+ Emballonura_monticola
+ Emballonura_raffrayana
+ Emballonura_semicaudata
+ Emballonura_serii
+ Emballonura_tiavato
+ Eonycteris_spelaea
+ Epomophorus_wahlbergi
+ Epomops_franqueti
+ Eptesicus_andersoni_andersoni
+ Eptesicus_andersoni_pallescens
+ Eptesicus_bottae_anatolicus
+ Eptesicus_bottae_hingstoni
+ Eptesicus_bottae_innesi
+ Eptesicus_bottae_ognevi
+ Eptesicus_bottae_taftanimontis
+ Eptesicus_diminutus
+ Eptesicus_fuscus
+ Eptesicus_hottentotus
+ Eptesicus_isabellinus_boscai
+ Eptesicus_isabellinus_isabellinus
+ Eptesicus_nasutus
+ Eptesicus_nilssoni
+ Eptesicus_regulus
+ Eptesicus_serotinus_mirza
+ Eptesicus_serotinus_turcomanus
+ Equus_caballus
+ Erinaceus_europaeus
+ Erophylla_bombifrons
+ Erophylla_sezekorni
+ Eumops_glaucinus_floridanus
+ Eumops_perotis
+ Eumops_sp__MMM_2008
+ Eumops_underwoodi
+ Felis_silvestris_catus
+ Furipterus_horrens
+ Glossophaga_commissarisi
+ Glossophaga_leachi
+ Glossophaga_longirostris
+ Glossophaga_morenoi
+ Glossophaga_soricina
+ Glyphonycteris_daviesi
+ Glyphonycteris_sylvestris
+ Haplonycteris_fischeri
+ Harpiocephalus_mordax
+ Harpyionycteris_whiteheadi
+ Hippopotamus_amphibius
+ Hipposideros_abae
+ Hipposideros_armiger
+ Hipposideros_ater
+ Hipposideros_beatus
+ Hipposideros_bicolor
+ Hipposideros_caffer
+ Hipposideros_calcaratus
+ Hipposideros_cervinus
+ Hipposideros_cineraceus
+ Hipposideros_coxi
+ Hipposideros_cyclops
+ Hipposideros_diadema
+ Hipposideros_dyacorum
+ Hipposideros_fuliginosus
+ Hipposideros_gigas
+ Hipposideros_jonesi
+ Hipposideros_khaokhouayensis
+ Hipposideros_larvatus
+ Hipposideros_pomona
+ Hipposideros_pratti
+ Hipposideros_ridleyi
+ Hipposideros_rotalis
+ Hipposideros_ruber
+ Hipposideros_sp__1_KS_2008
+ Hipposideros_speoris
+ Hypsugo_cadornae
+ Hypsugo_savii
+ Hypsugo_sp__C1
+ Hypsugo_sp__C2
+ Hypsugo_sp__C4
+ Ia_io
+ Idionycteris_phyllotis
+ Kerivoula_cf__papillosa
+ Laephotis_wintoni
+ Lasionycteris_noctivagans
+ Lasiurus_cinereus
+ Lasiurus_ega
+ Lasiurus_xanthinus
+ Leptonycteris_curasoae
+ Lionycteris_spurrelli
+ Lonchophylla_chocoana
+ Lonchophylla_handleyi
+ Lonchophylla_mordax
+ Lonchophylla_robusta
+ Lonchophylla_thomasi
+ Lonchorhina_aurita
+ Lophostoma_brasiliense
+ Lophostoma_evotis
+ Lophostoma_schulzi
+ Lophostoma_silvicola
+ Macroglossus_minimus
+ Macroglossus_sobrinus
+ Macrophyllum_macrophyllum
+ Macrotus_californicus
+ Macrotus_waterhousii
+ Manis_pentadactyla
+ Manis_tetradactyla
+ Megaderma_lyra
+ Megaderma_spasma
+ Megaerops_ecaudatus
+ Megaerops_niphanae
+ Megaerops_wetmorei
+ Megaloglossus_woermanni
+ Melonycteris_fardoulisi_fardoulisi
+ Melonycteris_fardoulisi_maccoyi
+ Melonycteris_fardoulisi_mengermani
+ Melonycteris_fardoulisi_schouteni
+ Melonycteris_melanops
+ Melonycteris_woodfordi_woodfordi
+ Mesophylla_macconnelli
+ Micronycteris_brachyotis
+ Micronycteris_brosseti
+ Micronycteris_cf__schmidtorum
+ Micronycteris_giovanniae
+ Micronycteris_hirsuta
+ Micronycteris_homezi
+ Micronycteris_matses
+ Micronycteris_megalotis
+ Micronycteris_microtis
+ Micronycteris_minuta
+ Micronycteris_nicefori
+ Micronycteris_schmidtorum
+ Micronycteris_sp__TK136752
+ Micropteropus_pusillus
+ Mimon_bennettii
+ Mimon_crenulatum
+ Miniopterus_africanus
+ Miniopterus_australis
+ Miniopterus_fraterculus
+ Miniopterus_fuliginosus
+ Miniopterus_gleni
+ Miniopterus_griveaudi
+ Miniopterus_griveaudi_griveaudi
+ Miniopterus_inflatus
+ Miniopterus_macrocneme
+ Miniopterus_magnater
+ Miniopterus_majori
+ Miniopterus_manavi
+ Miniopterus_minor
+ Miniopterus_natalensis
+ Miniopterus_newtonii
+ Miniopterus_petersoni
+ Miniopterus_schreibersii
+ Miniopterus_schreibersii_bassanii
+ Miniopterus_schreibersii_blepotis
+ Miniopterus_schreibersii_oceanensis
+ Miniopterus_schreibersii_orianae
+ Miniopterus_schreibersii_pallidus
+ Miniopterus_sp__BBRA_2009b
+ Miniopterus_sp__Comoros_clade_2
+ Miniopterus_sp__FMNH_167450
+ Miniopterus_sp__FMNH_172602
+ Miniopterus_sp__sororculus
+ Molossus_molossus
+ Monophyllus_plethodon
+ Monophyllus_redmani
+ Mops_condylurus
+ Mops_leucostigma
+ Mops_midas
+ Mormoops_blainvillii
+ Mormoops_megalophylla
+ Mormopterus_kalinowskii
+ Mosia_nigrescens
+ Murina_cf__cyclotis
+ Murina_leucogaster
+ Murina_sp__GGJ_2006
+ Murina_sp__hn1151
+ Myonycteris_brachycephala
+ Myonycteris_relicta
+ Myonycteris_torquata
+ Myotis_adversus
+ Myotis_albescens
+ Myotis_alcathoe
+ Myotis_altarium
+ Myotis_annectans
+ Myotis_atacamensis
+ Myotis_aurascens
+ Myotis_auriculus
+ Myotis_austroriparius
+ Myotis_bechsteinii
+ Myotis_blythii
+ Myotis_blythii_ancilla
+ Myotis_blythii_blythii
+ Myotis_blythii_omari
+ Myotis_blythii_oxygnathus
+ Myotis_blythii_punicus
+ Myotis_bocagei
+ Myotis_bombinus
+ Myotis_bombinus_amurensis
+ Myotis_brandtii
+ Myotis_californicus
+ Myotis_capaccinii
+ Myotis_cf__nipalensis_kukunorensis
+ Myotis_cf__pequinius
+ Myotis_cf__punicus
+ Myotis_chiloensis
+ Myotis_chinensis
+ Myotis_ciliolabrum
+ Myotis_dasycneme
+ Myotis_daubentoni
+ Myotis_daubentoni_nathalinae
+ Myotis_daubentonii_daubentonii
+ Myotis_davidii
+ Myotis_dominicensis
+ Myotis_elegans
+ Myotis_emarginatus
+ Myotis_escalerai
+ Myotis_evotis
+ Myotis_fimbriatus
+ Myotis_formosus
+ Myotis_formosus_flavus
+ Myotis_formosus_watasei
+ Myotis_frater
+ Myotis_goudoti
+ Myotis_gracilis
+ Myotis_grisescens
+ Myotis_hajastanicus
+ Myotis_hasseltii
+ Myotis_horsfieldii
+ Myotis_ikonnikovi
+ Myotis_keaysi
+ Myotis_keenii
+ Myotis_laniger
+ Myotis_latirostris
+ Myotis_leibii
+ Myotis_lesueuri
+ Myotis_levis
+ Myotis_longipes
+ Myotis_lucifugus
+ Myotis_lucifugus_alascensis
+ Myotis_lucifugus_carissima
+ Myotis_lucifugus_lucifugus
+ Myotis_lucifugus_relictus
+ Myotis_macrodactylus
+ Myotis_macropus
+ Myotis_macrotarsus
+ Myotis_martiniquensis
+ Myotis_montivagus
+ Myotis_muricola
+ Myotis_muricola_browni
+ Myotis_myotis
+ Myotis_myotis_myotis
+ Myotis_mystacinus
+ Myotis_nattereri
+ Myotis_nattereri_escalerae
+ Myotis_nattereri_tschuliensis
+ Myotis_nigricans
+ Myotis_nipalensis
+ Myotis_oxyotus
+ Myotis_pequinius
+ Myotis_petax
+ Myotis_pruinosus
+ Myotis_punicus
+ Myotis_ricketti
+ Myotis_riparius
+ Myotis_ruber
+ Myotis_schaubi
+ Myotis_scotti
+ Myotis_seabrai
+ Myotis_septentrionalis
+ Myotis_sicarius
+ Myotis_siligorensis
+ Myotis_simus
+ Myotis_sodalis
+ Myotis_sp__1_ZZ_2009
+ Myotis_sp__2_ZZ_2009
+ Myotis_sp__AM_M15111
+ Myotis_sp__C1
+ Myotis_sp__C2
+ Myotis_sp__C3
+ Myotis_sp__C4
+ Myotis_sp__C5
+ Myotis_sp__KK0005
+ Myotis_sp__PH_2006
+ Myotis_sp__XT_2007
+ Myotis_thysanodes
+ Myotis_tricolor
+ Myotis_velifer
+ Myotis_vivesi
+ Myotis_volans
+ Myotis_welwitschii
+ Myotis_yanbarensis
+ Myotis_yumanensis
+ Mystacina_tuberculata
+ Myzopoda_aurita
+ Myzopoda_schliemanni
+ Natalus_jamaicensis
+ Natalus_major
+ Natalus_saturatus
+ Natalus_stramineus
+ Natalus_tumidirostris
+ Neoromicia_brunneus
+ Neoromicia_capensis
+ Neoromicia_somalicus
+ Noctilio_albiventris
+ Noctilio_leporinus
+ Nyctalus_azoreum
+ Nyctalus_lasiopterus
+ Nyctalus_leisleri
+ Nyctalus_noctula
+ Nyctalus_plancyi
+ Nycticeius_humeralis
+ Nyctiellus_lepidus
+ Nyctimene_albiventer
+ Nyctimene_cephalotes
+ Nyctimene_major
+ Nyctimene_robinsoni
+ Nyctimene_vizcaccia
+ Nyctinomops_aurispinosus
+ Nyctinomops_laticaudatus
+ Otomops_cf__formosus
+ Otomops_madagascariensis
+ Otomops_martiensseni
+ Otomops_wroughtoni
+ Otopteropus_cartilagonodus
+ Penthetor_lucasi
+ Peropteryx_kappleri
+ Peropteryx_leucoptera
+ Peropteryx_macrotis
+ Peropteryx_sp__ROM_104396
+ Peropteryx_sp__RSV_2330
+ Peropteryx_trinitatis
+ Phylloderma_stenops
+ Phyllonycteris_aphylla
+ Phyllops_falcatus
+ Phyllostomus_hastatus
+ Pipistrellus_abramus
+ Pipistrellus_cf__javanicus
+ Pipistrellus_hesperidus
+ Pipistrellus_hesperus
+ Pipistrellus_kuhli
+ Pipistrellus_maderensis
+ Pipistrellus_nathusii
+ Pipistrellus_pipistrellus
+ Pipistrellus_pygmaeus
+ Pipistrellus_pygmaeus_x_mediterraneus
+ Pipistrellus_sp__Be_2129
+ Pipistrellus_sp__Be_2136_8
+ Pipistrellus_sp__Be_2137_9
+ Pipistrellus_sp__Be_2142_10
+ Pipistrellus_sp__Be_2145
+ Pipistrellus_sp__Be_2151_13
+ Pipistrellus_sp__Be_2152
+ Pipistrellus_sp__CO1
+ Pipistrellus_sp__CO2
+ Pipistrellus_sp__CO3
+ Pipistrellus_sp__PH_2007
+ Pipistrellus_subflavus
+ Platalina_genovensium
+ Platyrrhinus_albericoi
+ Platyrrhinus_aurarius
+ Platyrrhinus_brachycephalus
+ Platyrrhinus_dorsalis
+ Platyrrhinus_helleri
+ Platyrrhinus_helleri_incarum
+ Platyrrhinus_lineatus
+ Platyrrhinus_masu
+ Platyrrhinus_matapalensis
+ Platyrrhinus_recifinus
+ Platyrrhinus_vittatus
+ Plecotus_auritus
+ Plecotus_austriacus
+ Plecotus_balensis
+ Plecotus_cf__kolombatovici
+ Plecotus_christii
+ Plecotus_kolombatovici
+ Plecotus_macrobullaris
+ Plecotus_mexicanus
+ Plecotus_rafinesquii
+ Plecotus_rafinesquii2
+ Plecotus_sp__JJJ_2003
+ Plecotus_teneriffae
+ Promops_centralis
+ Ptenochirus_jagori
+ Ptenochirus_minor
+ Pteralopex_acrodonta
+ Pteronotus_davyi
+ Pteronotus_gymnonotus
+ Pteronotus_macleayii
+ Pteronotus_parnellii
+ Pteronotus_personatus
+ Pteronotus_pusillus
+ Pteronotus_quadridens
+ Pteronotus_rubiginosus
+ Pteropus_aldabrensis
+ Pteropus_alecto
+ Pteropus_conspicillatus
+ Pteropus_giganteus
+ Pteropus_hypomelanus
+ Pteropus_livingstonii
+ Pteropus_lylei
+ Pteropus_niger
+ Pteropus_poliocephalus
+ Pteropus_pumilus
+ Pteropus_rodricensis
+ Pteropus_rufus
+ Pteropus_scapulatus
+ Pteropus_seychellensis_comoroensis
+ Pteropus_seychellensis_seychellensis
+ Pteropus_speciosus
+ Pteropus_tonganus
+ Pteropus_vampyrus
+ Pteropus_voeltzkowi
+ Pygoderma_bilabiatum
+ Rhinolophus_acuminatus
+ Rhinolophus_affinis
+ Rhinolophus_blasii
+ Rhinolophus_blythi
+ Rhinolophus_borneensis
+ Rhinolophus_clivosus
+ Rhinolophus_cornutus
+ Rhinolophus_creaghi
+ Rhinolophus_darlingi
+ Rhinolophus_eloquens
+ Rhinolophus_euryale
+ Rhinolophus_ferrumequinum
+ Rhinolophus_formosae
+ Rhinolophus_fumigatus
+ Rhinolophus_hildebrandti
+ Rhinolophus_hipposideros
+ Rhinolophus_landeri
+ Rhinolophus_lepidus
+ Rhinolophus_luctus
+ Rhinolophus_macrotis
+ Rhinolophus_marshalli
+ Rhinolophus_mehelyi
+ Rhinolophus_monoceros
+ Rhinolophus_pearsonii
+ Rhinolophus_perditus
+ Rhinolophus_philippinensis
+ Rhinolophus_pumilus
+ Rhinolophus_pusillus
+ Rhinolophus_rex
+ Rhinolophus_sedulus
+ Rhinolophus_simulator
+ Rhinolophus_sinicus
+ Rhinolophus_sp__1_KS_2008
+ Rhinolophus_sp__2_KS_2008
+ Rhinolophus_stheno
+ Rhinolophus_thomasi
+ Rhinolophus_trifoliatus
+ Rhinolophus_xinanzhongguoensis
+ Rhinophylla_alethina
+ Rhinophylla_fischerae
+ Rhinophylla_pumilio
+ Rhinopoma_hardwickei
+ Rhinopoma_microphyllum
+ Rhinopoma_muscatellum
+ Rhogeessa_aeneus
+ Rhogeessa_genowaysi
+ Rhogeessa_gracilis
+ Rhogeessa_io
+ Rhogeessa_mira
+ Rhogeessa_parvula
+ Rhogeessa_tumida
+ Rhogeessa_velilla
+ Rhynchonycteris_naso
+ Rousettus_aegyptiacus
+ Rousettus_aegyptiacus_aegyptiacus
+ Rousettus_aegyptiacus_princeps
+ Rousettus_amplexicaudatus
+ Rousettus_angolensis
+ Rousettus_lanosus
+ Rousettus_leschenaultii
+ Rousettus_madagascariensis
+ Rousettus_spinalatus
+ Saccopteryx_bilineata
+ Saccopteryx_canescens
+ Saccopteryx_gymnura
+ Saccopteryx_leptura
+ Scotomanes_ornatus
+ Scotophilus_borbonicus
+ Scotophilus_dinganii
+ Scotophilus_heathii
+ Scotophilus_kuhlii
+ Scotophilus_leucogaster
+ Scotophilus_marovaza
+ Scotophilus_nigrita
+ Scotophilus_nux
+ Scotophilus_robustus
+ Scotophilus_tandrefana
+ Scotophilus_viridis
+ Scotophilus_viridis_nigritellus
+ Sphaeronycteris_toxophyllum
+ Stenoderma_rufum
+ Sturnira_aratathomasi
+ Sturnira_bidens
+ Sturnira_bogotensis
+ Sturnira_erythromos
+ Sturnira_ludovici
+ Sturnira_luisi_angeli
+ Sturnira_luisi_paulsoni
+ Sturnira_luisi_serotinus
+ Sturnira_luisi_thomasi
+ Sturnira_luisi_vulcanensis
+ Sturnira_luisi_zygomaticus
+ Sturnira_magna
+ Sturnira_mordax
+ Sturnira_nana
+ Sturnira_oporaphilum
+ Sturnira_sp__CAI_2003A
+ Sturnira_sp__CAI_2003B
+ Sturnira_tildae
+ Syconycteris_sp
+ Tadarida_brasiliensis
+ Tadarida_fulminans
+ Tadarida_teniotis
+ Talpa_altaica
+ Taphozous_longimanus
+ Taphozous_melanopogon
+ Tapirus_indicus
+ Thyroptera_tricolor
+ Tomopeas_ravus
+ Tonatia_bidens
+ Tonatia_saurophila
+ Trachops_cirrhosus
+ Triaenops_afer
+ Triaenops_auritus
+ Triaenops_furculus
+ Triaenops_persicus
+ Triaenops_rufus
+ Triaenops_sp__PPV_2008
+ Tylonycteris_pachypus
+ Uroderma_bilobatum
+ Uroderma_magnirostrum
+ Vampyressa_bidens
+ Vampyressa_brocki
+ Vampyressa_melissa
+ Vampyressa_nymphaea
+ Vampyressa_pusilla
+ Vampyressa_thyone
+ Vampyrodes_caraccioli
+ Vampyrum_spectrum
+ Vespertilio_murinus
+ Vespertilio_sinensis
+ ;
+END;
+
+BEGIN TREES;
+ TITLE Bayesian_Result;
+ LINK TAXA = Taxa;
+ TREE Fig._1 = [&R] 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ifugus:0.008413)1.00:0.021815,((Myotis_lucifugus_relictus:0.00489,Myotis_lucifugus_carissima:0.002335)1.00:0.006842,(Myotis_thysanodes:0.022321,(Myotis_keenii:0.010361,Myotis_evotis:0.004178)0.78:0.002919)0.46:0.002249)0.40:0.003454)1.00:0.022446)1.00:0.044966)1.00:0.029624)0.79:0.019826)1.00:0.054127,((Myotis_brandtii:0.101471,(Myotis_aurascens:0.204371,(Myotis_gracilis:0.003707,Myotis_sp__KK0005:3.53E-4)1.00:0.036111)0.88:0.070176)0.87:0.042852,((Myotis_keaysi:0.077243,(Myotis_ruber:0.083952,(Myotis_simus:0.019349,(Myotis_elegans:0.017721,Myotis_riparius:0.031111)0.83:0.011611)1.00:0.041868)1.00:0.044439)1.00:0.056583,(Myotis_vivesi:0.221431,((Myotis_martiniquensis:0.071724,(Myotis_atacamensis:0.056247,Myotis_dominicensis:0.062661)0.66:0.007801)1.00:0.016688,((Myotis_grisescens:0.058806,Myotis_austroriparius:0.066103)0.87:0.020182,((Myotis_velifer:0.039432,Myotis_yumanensis:0.054323)1.00:0.03883,(Myotis_chiloensis:0.072855,(Myotis_albescens:0.078999,(Myotis_oxyotus:0.022359,(Myotis_levis:0.032793,Myotis_nigricans:0.02598)1.00:0.021462)1.00:0.051257)1.00:0.024781)0.87:0.021855)0.86:0.012252)0.53:0.004711)0.87:0.021874)0.87:0.031151)0.87:0.0269)0.87:0.023535)0.87:0.039636,((Myotis_latirostris:0.098138,Myotis_sp__PH_2006:0.089727)1.00:0.226562,((((Myotis_bocagei:0.250697,Myotis_welwitschii:0.158145)0.80:0.018413,(Myotis_formosus:0.009228,Myotis_formosus_watasei:0.001509)1.00:0.169929)0.95:0.037358,(Myotis_scotti:0.175217,(Myotis_goudoti:0.135099,(Myotis_emarginatus:0.085993,(Myotis_tricolor:0.129874,(Myotis_formosus_flavus:0.006326,Myotis_sp__XT_2007:0.00271)1.00:0.161619)0.73:0.023319)0.74:0.017895)0.43:0.012542)0.56:0.022314)0.87:0.086902,(Myotis_alcathoe:0.228974,((Myotis_dasycneme:0.184769,(Myotis_muricola:0.171121,((Myotis_nipalensis:0.07344,Myotis_mystacinus:0.110812)0.49:0.031847,(Myotis_altarium:0.136333,Myotis_ikonnikovi:0.06389)1.00:0.05328)0.95:0.034831)0.85:0.02146)0.69:0.009945,((Myotis_capaccinii:0.19135,(Myotis_muricola_browni:0.145375,(Myotis_horsfieldii:0.130935,((Myotis_sp__AM_M15111:0.061961,Myotis_macrotarsus:0.090489)0.60:0.043537,(Myotis_hasseltii:0.075268,Myotis_macropus:0.090422)0.71:0.016464)0.59:0.024289)0.63:0.061192)0.59:0.020446)0.21:0.0031,((Myotis_annectans:0.251254,(Myotis_pruinosus:0.166674,(Myotis_montivagus:0.149664,Myotis_yanbarensis:0.154124)0.43:0.008538)1.00:0.051196)0.63:0.050929,((Myotis_sp__2_ZZ_2009:0.121621,((Myotis_laniger:0.009653,Myotis_longipes:0.016374)1.00:0.058384,(Myotis_davidii:0.022292,(Myotis_siligorensis:0.027391,Myotis_sp__1_ZZ_2009:0.02078)0.98:0.013713)1.00:0.029495)1.00:0.082083)1.00:0.072473,(((Myotis_sicarius:0.134589,(Myotis_bechsteinii:0.160801,(Myotis_frater:0.098077,(Myotis_daubentonii_daubentonii:0.008684,Myotis_daubentoni_nathalinae:0.007956)1.00:0.10848)0.62:0.021754)0.70:0.023222)1.00:0.057872,((Myotis_fimbriatus:0.095761,(Myotis_adversus:0.025269,Myotis_ricketti:0.033805)1.00:0.048691)1.00:0.053166,(Myotis_macrodactylus:0.136785,(Myotis_hajastanicus:0.171281,(Myotis_daubentoni:0.018352,Myotis_petax:0.006195)1.00:0.026172)0.50:0.047486)0.41:0.017931)0.50:0.070026)0.50:0.015621,(((Myotis_cf__punicus:0.013588,(Myotis_punicus:0.005463,Myotis_blythii_punicus:0.003122)0.84:0.008754)1.00:0.097315,((Myotis_blythii_ancilla:0.008967,Myotis_blythii_blythii:0.019671)1.00:0.032017,((Myotis_blythii_omari:0.018776,Myotis_blythii_oxygnathus:0.006252)1.00:0.016343,(Myotis_myotis:0.002134,(Myotis_blythii:0.002843,Myotis_myotis_myotis:7.11E-4)0.97:0.004596)0.98:0.01011)1.00:0.023565)1.00:0.048281)1.00:0.027783,(Myotis_chinensis:0.138486,(((Myotis_pequinius:0.052279,Myotis_cf__pequinius:0.061923)0.75:0.022408,(Myotis_nattereri:0.0231,(Myotis_bombinus_amurensis:0.020074,Myotis_bombinus:0.003755)1.00:0.022231)1.00:0.047621)1.00:0.060306,((Myotis_nattereri_tschuliensis:0.025371,Myotis_schaubi:0.024015)1.00:0.084327,((Myotis_escalerai:0.008676,Myotis_nattereri_escalerae:0.001271)1.00:0.049149,(Myotis_sp__C1:0.007718,(Myotis_sp__C5:0.006641,(Myotis_sp__C4:0.001925,(Myotis_sp__C2:0.001751,Myotis_sp__C3:0.00341)0.91:0.003316)0.91:0.004416)1.00:0.013568)1.00:0.065933)1.00:0.053086)1.00:0.048155)1.00:0.029672)1.00:0.021885)1.00:0.062966)0.23:0.00606)0.37:0.01397)0.20:0.011355)0.50:0.02473)0.50:0.017697)0.31:0.018119)0.50:0.036524)0.23:0.011782)0.50:0.042293)0.50:0.029586)0.50:0.060592)0.50:0.13413)0.50:0.069651)0.50:0.061496)0.30:0.076821)0.50:0.062648)0.50:0.094058)0.50:0.039525)0.50:0.281791)0.63:0.086525)0.50:0.132368)0.98:0.59788);
+[! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr48974]
+
+
+END;
View
4 Tests/test_Phylo.py
@@ -17,6 +17,7 @@
EX_NEWICK = 'Nexus/int_node_labels.nwk'
EX_NEWICK2 = 'Nexus/test.new'
EX_NEXUS = 'Nexus/test_Nexus_input.nex'
+EX_NEXUS2 = 'Nexus/bats.nex'
# Example PhyloXML files
EX_APAF = 'PhyloXML/apaf.xml'
@@ -37,6 +38,9 @@ def test_newick_read_single(self):
self.assertEqual(tree.find_any('Homo sapiens').comment, 'modern human')
self.assertEqual(tree.find_any('Equus caballus').comment, "wild horse; also 'Equus ferus caballus'")
self.assertEqual(tree.root.confidence, 1.0)
+
+ tree = Phylo.read(EX_NEXUS2, 'nexus')
+ self.assertEqual(len(tree.get_terminals()), 658)
def test_newick_read_multiple(self):
"""Parse a Nexus file with multiple trees."""
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