Added a rooted version of the orthomam tree.

b393eec5 · BOUSSAU Bastien · Philippe Veber · b00aa6f2 · b393eec5
Commit b393eec5 authored Nov 03, 2020 by BOUSSAU Bastien Committed by Philippe Veber Nov 03, 2020
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example/trees_test/orthomam_rooted.nhx example/trees_test/orthomam_rooted.nhx +1 -0

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--- a/example/trees_test/orthomam_rooted.nhx
+++ b/example/trees_test/orthomam_rooted.nhx
+(Ornithorhynchus_anatinus:0.09545,((Monodelphis_domestica:0.02526,((Notamacropus_eugenii:0.01950,Phascolarctos_cinereus:0.01419)[&&NHX:Condition=0]:0.00315,Sarcophilus_harrisii:0.01825)[&&NHX:Condition=0]:0.00694)[&&NHX:Condition=0]:0.04245,(((Choloepus_hoffmanni:0.02618,Dasypus_novemcinctus:0.02125)[&&NHX:Condition=0]:0.01083,((((Chrysochloris_asiatica:0.02571,Echinops_telfairi:0.05058)[&&NHX:Condition=0]:0.00363,Elephantulus_edwardii:0.03755)[&&NHX:Condition=0]:0.00084,Orycteropus_afer_afer:0.02186)[&&NHX:Condition=0]:0.00253,((Loxodonta_africana:0.01495,Procavia_capensis:0.03119)[&&NHX:Condition=0]:0.00173,Trichechus_manatus_latirostris:0.01557)[&&NHX:Condition=0]:0.00589)[&&NHX:Condition=0]:0.00868)[&&NHX:Condition=0]:0.00073,((((((((Aotus_nancymaae:0.00375,Callithrix_jacchus:0.00587)[&&NHX:Condition=0]:0.00052,(Cebus_capucinus:0.00482,Saimiri_boliviensis:0.00441)[&&NHX:Condition=0]:0.00053)[&&NHX:Condition=0]:0.00841,((((((Cercocebus_atys:0.00099,Mandrillus_leucophaeus:0.00113)[&&NHX:Condition=0]:0.00025,Papio_anubis:0.00116)[&&NHX:Condition=0]:0.00011,((Macaca_fascicularis:0.00060,Macaca_mulatta:0.00034)[&&NHX:Condition=0]:0.00039,Macaca_nemestrina:0.00075)[&&NHX:Condition=0]:0.00049)[&&NHX:Condition=0]:0.00032,Chlorocebus_sabaeus:0.00261)[&&NHX:Condition=0]:0.00090,((Colobus_angolensis:0.00203,Piliocolobus_tephrosceles:0.00202)[&&NHX:Condition=0]:0.00048,(Rhinopithecus_bieti:0.00063,Rhinopithecus_roxellana:0.00075)[&&NHX:Condition=0]:0.00143)[&&NHX:Condition=0]:0.00099)[&&NHX:Condition=0]:0.00270,(((Gorilla_gorilla:0.00158,(Homo_sapiens:0.00090,(Pan_paniscus:0.00075,Pan_troglodytes:0.00100)[&&NHX:Condition=0]:0.00094)[&&NHX:Condition=0]:0.00038)[&&NHX:Condition=0]:0.00167,Pongo_abelii:0.00395)[&&NHX:Condition=0]:0.00025,Nomascus_leucogenys:0.00502)[&&NHX:Condition=0]:0.00133)[&&NHX:Condition=0]:0.00264)[&&NHX:Condition=0]:0.01009,Carlito_syrichta:0.02301)[&&NHX:Condition=0]:0.00175,((Microcebus_murinus:0.00961,Propithecus_coquereli:0.00700)[&&NHX:Condition=0]:0.00678,Otolemur_garnettii:0.02195)[&&NHX:Condition=0]:0.00642)[&&NHX:Condition=0]:0.00171,Galeopterus_variegatus:0.02262)[&&NHX:Condition=0]:0.00084,((((((Castor_canadensis:0.02073,Dipodomys_ordii:0.03328)[&&NHX:Condition=0]:0.00445,((((((Cricetulus_griseus:0.00798,Mesocricetus_auratus:0.01095)[&&NHX:Condition=0]:0.00555,Microtus_ochrogaster:0.01763)[&&NHX:Condition=0]:0.00116,Peromyscus_maniculatus:0.01328)[&&NHX:Condition=0]:0.00431,(Meriones_unguiculatus:0.02190,(((Mus_caroli:0.00383,(Mus_musculus:0.00111,Mus_spretus:0.00175)[&&NHX:Condition=0]:0.00182)[&&NHX:Condition=0]:0.00398,Mus_pahari:0.00780)[&&NHX:Condition=0]:0.00693,Rattus_norvegicus:0.01651)[&&NHX:Condition=0]:0.01040)[&&NHX:Condition=0]:0.00318)[&&NHX:Condition=0]:0.01443,Nannospalax_galili:0.02147)[&&NHX:Condition=0]:0.00572,Jaculus_jaculus:0.03645)[&&NHX:Condition=0]:0.00607)[&&NHX:Condition=0]:0.00251,(((Cavia_aperea:0.00280,Cavia_porcellus:0.00096)[&&NHX:Condition=0]:0.02192,(Chinchilla_lanigera:0.01277,Octodon_degus:0.02114)[&&NHX:Condition=0]:0.00307)[&&NHX:Condition=0]:0.00400,(Fukomys_damarensis:0.01684,Heterocephalus_glaber:0.01383)[&&NHX:Condition=0]:0.00850)[&&NHX:Condition=0]:0.01928)[&&NHX:Condition=0]:0.00058,(Ictidomys_tridecemlineatus:0.00304,Marmota_marmota_marmota:0.00259)[&&NHX:Condition=0]:0.02046)[&&NHX:Condition=0]:0.00471,(Ochotona_princeps:0.03724,Oryctolagus_cuniculus:0.01612)[&&NHX:Condition=0]:0.01439)[&&NHX:Condition=0]:0.00150,(Tupaia_belangeri:0.00400,Tupaia_chinensis:0.00064)[&&NHX:Condition=0]:0.02676)[&&NHX:Condition=0]:0.00059)[&&NHX:Condition=0]:0.00332,((Condylura_cristata:0.02938,(Erinaceus_europaeus:0.04161,Sorex_araneus:0.04776)[&&NHX:Condition=0]:0.00541)[&&NHX:Condition=0]:0.00599,((((Eptesicus_fuscus:0.00778,((Myotis_brandtii:0.00153,Myotis_lucifugus:0.00235)[&&NHX:Condition=1]:0.00133,Myotis_davidii:0.00563)[&&NHX:Condition=1]:0.00546)[&&NHX:Condition=1]:0.01256,Miniopterus_natalensis:0.01754)[&&NHX:Condition=1]:0.01075,((Hipposideros_armiger:0.01394,Rhinolophus_sinicus:0.01233)[&&NHX:Condition=1]:0.00776,((Pteropus_alecto:0.00070,Pteropus_vampyrus:0.00304)&&NHX:Transition=0:Condition=0:0.00546,Rousettus_aegyptiacus:0.00734)[&&NHX:Condition=1]:0.01556)[&&NHX:Condition=1]:0.00140)&&NHX:Transition=1:Condition=1:0.00470,((((((Balaenoptera_acutorostrata_scammoni:0.00580,(((Delphinapterus_leucas:0.00260,(Orcinus_orca:0.00078,Tursiops_truncatus:0.00240)[&&NHX:Condition=1]:0.00188)[&&NHX:Condition=1]:0.00121,Lipotes_vexillifer:0.00403)[&&NHX:Condition=1]:0.00254,Physeter_catodon:0.00660)[&&NHX:Condition=1]:0.00097)&&NHX:Transition=1:Condition=1:0.00881,(((((Bison_bison_bison:0.00093,Bos_mutus:0.00100)[&&NHX:Condition=0]:0.00020,(Bos_indicus:0.00027,Bos_taurus:0.00058)[&&NHX:Condition=0]:0.00044)[&&NHX:Condition=0]:0.00209,Bubalus_bubalis:0.00313)[&&NHX:Condition=0]:0.00261,((Capra_hircus:0.00141,Ovis_aries:0.00187)[&&NHX:Condition=0]:0.00111,Pantholops_hodgsonii:0.00329)[&&NHX:Condition=0]:0.00334)[&&NHX:Condition=0]:0.00142,Odocoileus_virginianus_texanus:0.00770)[&&NHX:Condition=0]:0.01461)[&&NHX:Condition=0]:0.00342,Sus_scrofa:0.01780)[&&NHX:Condition=0]:0.00174,(((Camelus_bactrianus:0.00021,Camelus_ferus:0.00044)[&&NHX:Condition=0]:0.00045,Camelus_dromedarius:0.00048)[&&NHX:Condition=0]:0.00241,Vicugna_pacos:0.00666)[&&NHX:Condition=0]:0.01424)[&&NHX:Condition=0]:0.00660,(Ceratotherium_simum_simum:0.01127,(Equus_asinus:0.00162,(Equus_caballus:0.00097,Equus_przewalskii:0.00034)[&&NHX:Condition=0]:0.00057)[&&NHX:Condition=0]:0.01128)[&&NHX:Condition=0]:0.00660)[&&NHX:Condition=0]:0.00036,(Manis_javanica:0.03079,((((Ailuropoda_melanoleuca:0.00537,Ursus_maritimus:0.00365)[&&NHX:Condition=0]:0.00603,((Enhydra_lutris_kenyoni:0.00314,Mustela_putorius:0.00430)[&&NHX:Condition=0]:0.00765,((Leptonychotes_weddellii:0.00254,Neomonachus_schauinslandi:0.00150)[&&NHX:Condition=0]:0.00373,Odobenus_rosmarus_divergens:0.00587)[&&NHX:Condition=0]:0.00419)[&&NHX:Condition=0]:0.00075)[&&NHX:Condition=0]:0.00267,Canis_familiaris:0.01365)[&&NHX:Condition=0]:0.00263,((Panthera_pardus:0.00074,Panthera_tigris_altaica:0.00045)[&&NHX:Condition=0]:0.00063,(Acinonyx_jubatus:0.00181,Felis_catus:0.00093)[&&NHX:Condition=0]:0.00018)[&&NHX:Condition=0]:0.00998)[&&NHX:Condition=0]:0.00680)[&&NHX:Condition=0]:0.00231)[&&NHX:Condition=0]:0.00042)[&&NHX:Condition=0]:0.00124)[&&NHX:Condition=0]:0.00422)[&&NHX:Condition=0]:0.00337)[&&NHX:Condition=0]:0.04848):0.00647);