From: cmzmasek@gmail.com Date: Thu, 17 Jul 2014 20:07:13 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1dd7ca838366105277ac62033a1f84bd85c94dc3;p=jalview.git in progress --- diff --git a/forester/aptx/aptx_example_files/amphi_frost.phyloxml b/forester/aptx/aptx_example_files/amphi_frost.phyloxml deleted file mode 100644 index 48f4ffb..0000000 --- a/forester/aptx/aptx_example_files/amphi_frost.phyloxml +++ /dev/null @@ -1,4791 +0,0 @@ - - - - - - - - - Latimeria chalumnae 1114 - - - - - - - - - - - - - - frogs - - - - - - - - - - - - - - - - - - - - - - - - - - - - Hemiphractus helioi 467 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Melanophryniscus klappenbachi 217 - - - - - - - - - - - Dendrophryniscus minutus 532 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Bufo variegatus 951 - - - - - - - - - - - Bufo amboroensis TJ32 - - - - - - - - Bufo arenarum 567 - - - - - - - - Bufo marinus 523 - - - - - Bufo paracnemis 564 - - - - - - - - - - - Bufo spinulosus 433 - - - - - Bufo granulosus TJ1 - - - - - - - - - - - - - - Bufo mazatlanensis - - - - - Bufo nebulifer - - - - - - - - - Bufo coniferus 955 - - - - - Bufo alvarius 1054 - - - - - - - - - - - Bufo boreas 967 - - - - - - - - Bufo punctatus 949 - - - - - - - - Bufo quercicus 940 - - - - - - - - Bufo cognatus 946 - - - - - - - - Bufo terrestris 945 - - - - - Bufo woodhousii 974 - - - - - - - - - - - - - - - - - - - - Bufo brauni TJ63 - - - - - - - - Bufo tuberosus TJ127 - - - - - - - - - - - Bufo camerunensis TJ121 - - - - - - - - Bufo regularis 952 - - - - - Bufo gutturalis TJ84 - - - - - - - - - - Bufo latifrons TJ108 - - - - - Bufo maculatus TJ34 - - - - - - - - - - - - Bufo angusticeps - - - - - Stephopaedes anotis - - - - - - - - - - Capensibufo rosei - - - - - Capensibufo tradouwi - - - - - - - - - - - Bufo bufo - - - - - - - - Bufo andrewsi 1016 - - - - - Torrentophryne aspinia - - - - - - - - - - - Bufo viridis 1063 - - - - - - - - Bufo melanostictus TJ10 - - - - - - - - Bufo lemur 1058 - - - - - Schismaderma carens TJ73 - - - - - - - - - - - - - - - - - - Bufo celebensis - - - - - - - - Bufo galeatus TJ20 - - - - - - - - Bufo divergens 936 - - - - - Bufo biporcatus - - - - - - - - - - - Pelophryne brevipes - - - - - - - - Bufo margaritifer - - - - - Rhamphophryne festae - - - - - - - - - - - - - - Nectophrynoides tornieri TJ60 - - - - - Didynamipus sjostedti - - - - - - - - - Ansonia longidigitata TJ106 - - - - - Ansonia muelleri - - - - - - - - - - - - Bufo asper 935 - - - - - Pedostibes hosei 953 - - - - - - - - - - Wolterstorffina parvipalmata TJ110 - - - - - - - - Werneria mertensi TJ114 - - - - - - - - Nectophryne batesi 958 - - - - - Nectophryne afra TJ124 - - - - - - - - - - - - Bufo haematiticus 956 - - - - - Bufo guttatus TJ2 - - - - - - - - - - - Osornophryne guacamayo - - - - - - - - Atelopus zeteki 1039 - - - - - - - - Atelopus flavescens 1046 - - - - - Atelopus spumarius 1047 - - - - - - - - - - - - - Thoropa miliaris 1186 - - - - - - - - - - - - - - Phyllobates lugubris 329 - - - - - - - - Minyobates claudiae 324 - - - - - Dendrobates auratus 327 - - - - - - - - - - Ameerega boulengeri 280 - - - - - Phobobates silverstonei 646 - - - - - - - - - - Mannophryne trinitatis 609 - - - - - - - - Colostethus undulatus 332 - - - - - Allobates femoralis 394 - - - - - - - - - - - - - - - - - - - - - - Limnomedusa macroglossa 681 - - - - - - - - Proceratophrys avelinoi 306 - - - - - - - - Odontophrynus americanus 309 - - - - - Odontophrynus achalensis 869 - - - - - - - - - - - Hylorina sylvatica - - - - - - - - Alsodes gargola 653 - - - - - Eupsophus calcaratus 657 - - - - - - - - - - - Cycloramphus boraceiensis 890 - - - - - Rhinoderma darwinii 1115 - - - - - - - - - - Crossodactylus schmidti 149 - - - - - - - - Megaelosia goeldii 611 - - - - - Hylodes phyllodes 889 - - - - - - - - - - - - - - - - - - Lepidobatrachus laevis 939 - - - - - - - - Ceratophrys cranwelli 539 - - - - - Chacophrys pierottii 1184 - - - - - - - - - - Batrachyla leptopus 655 - - - - - Atelognatus patagonicus 656 - - - - - - - - - - Telmatobius simonsi 314 - - - - - - - - Telmatobius cf jahuira 313 - - - - - Telmatobius sp 315 - - - - - - - - - - - - - - - - - - Pseudopaludicola sp 650 - - - - - - - - - - - - - - Leptodactylus fuscus TJ50 - - - - - - - - Leptodactylus ocellatus 568 - - - - - Vanzolinius discodactylus TJ81 - - - - - - - - - - Adenomera hylaedactyla 529 - - - - - Lithodytes lineatus 632 - - - - - - - - - - Paratelmatobius sp 891 - - - - - Scythrophrys sawayae 892 - - - - - - - - - - - Pleurodema brachyops 630 - - - - - - - - Edalorhina perezi 531 - - - - - Physalaemus cuvieri TJ65 - - - - - - - - - - - Allophryne ruthveni 837 - - - - - - - - Hyalinobatrachium fleischmanni TJ97 - - - - - - - - Centrolene prosoblepon 827 - - - - - - - - Cochranella bejaranoi 311 - - - - - Centrolene geckoideum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Charadrahyla nephila 551 - - - - - - - - - - - - - - - - - Smilisca phaeota 459 - - - - - - - - Triprion petasatus 458 - - - - - Anotheca spinosa 552 - - - - - - - - - - Hyla cinerea 207 - - - - - Tlalocohyla picta 658 - - - - - - - - - - Isthmohyla rivularis 210 - - - - - Hyla arborea 871 - - - - - - - - - - - - - Acris crepitans 604 - - - - - - - - Pseudacris crucifer 638 - - - - - Pseudacris triseriata 833 - - - - - - - - - - Exerodonta chimalapa 549 - - - - - Plectrohyla guatemalensis 802 - - - - - - - - - - - - Ecnomiohyla miliaria 639 - - - - - - - - Duellmanohyla rufioculis 211 - - - - - Ptychohyla leonhardschultzei 796 - - - - - - - - - - - Phyllodytes luteolus 823 - - - - - - - - - - - Argenteohyla siemersi pederseni 292 - - - - - - - - Trachycephalus venulosus 94 - - - - - Trachycephalus jordani 540 - - - - - - - - - - Osteopilus septentrionalis 139 - - - - - Osteocephalus cf taurinus 410 - - - - - - - - - - - - - - - Dendropsophus minutus 35 - - - - - - - - Dendropsophus marmoratus 468 - - - - - - - - Dendropsophus parviceps 80 - - - - - Dendropsophus nana 172 - - - - - - - - - - - Scarthyla goinorum 86 - - - - - - - - Lysapsus laevis 629 - - - - - Pseudis paradoxa 704 - - - - - - - - - - - - - - - - - - Hypsiboas granosus 416 - - - - - - - - - - - Hypsiboas multifasciata 102 - - - - - Hypsiboas boans 486 - - - - - - - - - Aplastodiscus perviridis 4 - - - - - Hypsiboas albomarginata 140 - - - - - - - - - - - Hyloscirtus armata 318 - - - - - Hyloscirtus palmeri 504 - - - - - - - - - - Sphaenorhynchus lacteus 138 - - - - - - - - Scinax ruber 16 - - - - - Scinax garbei 90 - - - - - - - - - - - - - - - - - - Nyctimistes pulchra 676 - - - - - - - - - - - - - - Litoria lesueurii 988 - - - - - Litoria genimaculata 1004 - - - - - - - - - Litoria aurea 543 - - - - - Cyclorana australis 674 - - - - - - - - - - Litoria nannotis 1000 - - - - - Nyctimystes dayi 1002 - - - - - - - - - - - Litoria meiriana 675 - - - - - - - - Litoria freycineti 672 - - - - - Litoria inermis 995 - - - - - - - - - - - - - - Phyllomedusa vaillanti 103 - - - - - Agalychnis calcarifer 1006 - - - - - - - - - Phasmahyla guttata 687 - - - - - Agalychnis callidryas TJ71 - - - - - - - - - - - - - Flectonotus sp 690 - - - - - - - - Gastrotheca cf marsupiata 317 - - - - - Gastrotheca fissipes 825 - - - - - - - - - - - Stefania evansi 417 - - - - - Cryptobatrachus sp - - - - - - - - - - - - - - - - - - - Craugastor bufoniformis 954 - - - - - - - - - - - Craugastor rhodopis 1088 - - - - - - - - Craugastor ranoides 897 - - - - - Craugastor punctariolus 957 - - - - - - - - - - Craugastor augusti 1056 - - - - - Craugastor alfredi 1089 - - - - - - - - - - - Phrynopus sp TJ30 - - - - - Phrynopus sp KU 202652 - - - - - - - - - - Craugastor pluvicanorus TJ31 - - - - - - - - Euhyas planirostris 898 - - - - - - - - Syrrhophus marnockii 894 - - - - - Syrrhophus nitidus 1087 - - - - - - - - - - - - - - - Barycholos ternetzi 887 - - - - - - - - Brachycephalus ephippium 883 - - - - - Eleutherodactylus juipoca 886 - - - - - - - - - - Ischnocnema sp 521 - - - - - Eleutherodactylus binotatus 884 - - - - - - - - - - - - - - - - - - - - - - Taudactylus acutirostris 1062 - - - - - - - - - - - - - - - - - Myobatachus gouldii 1081 - - - - - - - - Metacrinia nichollsi 1071 - - - - - Arenophryne sp 1155 - - - - - - - - - - Pseudophryne bibroni 677 - - - - - Pseudophryne coriacea 1082 - - - - - - - - - - Uperoleia laevigata 1003 - - - - - Spicospina flammocaerulea 1075 - - - - - - - - - - - - - Paracrinia haswelli 1077 - - - - - - - - Assa darlingtoni 1066 - - - - - Geocrinia victoriana 1072 - - - - - - - - - - Crinia signifera 978 - - - - - Bryobatrachus nimbus 1074 - - - - - - - - - - - - Rheobatrachus silus 1061 - - - - - Mixophyes carbinensis 1086 - - - - - - - - - - Kyarranus sphagnicolus 1084 - - - - - - - - Adelotus brevis 1073 - - - - - - - - - - - Heleioporus australiacus 1079 - - - - - - - - Limnodynastes dumerilli 1067 - - - - - - - - - - - Megistolotis lignarius 1069 - - - - - Limnodynastes salmini - - - - - - - - - Limnodynastes peronii 1032 - - - - - Limnodynastes depressus 1080 - - - - - - - - - - - - - - - Notaden melanoscaphus 1068 - - - - - - - - Limnodynastes ornatus 1064 - - - - - Lechriodus fletcheri 1065 - - - - - - - - - - Neobatrachus sudelli 673 - - - - - Neobatrachus pictus 1070 - - - - - - - - - - - - - - Telmatobufo venustus 1131 - - - - - Caudiverbera caudiverbera TJ87 - - - - - - - - - - - - - - Nasikabatrachus sahyadrensis - - - - - Nasikabatrachidae sp - - - - - - - - - Sooglossus sechellensis TJ94 - - - - - Nesomantis thomasseti TJ96 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Staurois tuberlinguis 927 - - - - - - - - - - - - - - - - - Glandirana minima - - - - - - - - - - - - - - - - - - - - Rana sylvatica TJ33 - - - - - - - - - - - Pantherana capito 973 - - - - - - - - - - - Pantherana berlandieri - - - - - - - - Pantherana forreri 895 - - - - - Pantherana yavapaiensis 1057 - - - - - - - - - - Pantherana pipiens 913 - - - - - Pantherana chiricahuensis 1055 - - - - - - - - - - - Lithobates palmipes TJ28 - - - - - - - - Trypheropsis warszewitschii 1043 - - - - - Sierrana maculata 1076 - - - - - - - - - - - - Aquarana grylio 972 - - - - - - - - Aquarana heckscheri 977 - - - - - - - - Aquarana clamitans 971 - - - - - Aquarana catesbeiana 1044 - - - - - - - - - - - - - - - Pseudorana johnsi 997 - - - - - - - - Rana japonica 923 - - - - - - - - Pseudoamalops sauteri 914 - - - - - Rana temporaria 916 - - - - - - - - - - - Aurorana aurora 975 - - - - - Amerana mucosa 976 - - - - - - - - - - - - - - - - - Huia nasica TJ11 - - - - - Odorrana livida TJ38 - - - - - - - - - Odorrana grahami 1025 - - - - - Amolops chapaensis TJ17 - - - - - - - - - - Nidirana adenopleura 908 - - - - - Nidirana chapaensis TJ13 - - - - - - - - - - - Amolops hongkongensis - - - - - - - - Pelophylax nigromaculata 924 - - - - - Pelophylax ridibunda - - - - - - - - - - - - Meristogenys orphnocnemis 934 - - - - - Clinotarsus curtipes - - - - - - - - - - - - - - - - Sylvirana temporalis - - - - - - - - Papurana daemeli 985 - - - - - Tylerana arfaki 987 - - - - - - - - - - Sylvirana nigrovittata TJ16 - - - - - Sylvirana maosonensis TJ18 - - - - - - - - - - Chalcorana chalconota 926 - - - - - - - - Amnirana galamensis 512 - - - - - Amnirana albilabris TJ131 - - - - - - - - - - - - Sylvirana guentheri 1052 - - - - - - - - Hylarana erythraea 925 - - - - - Hylarana taipehensis TJ40 - - - - - - - - - - - - Lankanectes corrugatus - - - - - - - - Nyctibatrachus cf aliciae - - - - - Nyctibatrachus major - - - - - - - - - - - - - - Buergeria japonica 502 - - - - - - - - Philautus gracilipes 446 - - - - - - - - - - - - - - - - - - - - Chirixalus vittatus 921 - - - - - - - - Chirixalus doriae 922 - - - - - Chiromantis xerampelina TJ42 - - - - - - - - - - Polypedates leucomystax 442 - - - - - Polypedates cruciger - - - - - - - - - - Rhacophorus annamensis 441 - - - - - - - - Rhacophorus bipunctatus 440 - - - - - - - - Rhacophorus orlovi 443 - - - - - Rhacophorus calcaneus TJ24 - - - - - - - - - - - - - - - Theloderma corticale 445 - - - - - Philautus rhododiscus TJ37 - - - - - - - - - Nyctixalus 905 - - - - - Nyctixalus pictus 920 - - - - - - - - - - - Chirixalus idiooticus 500 - - - - - Chirixalus eiffingeri 912 - - - - - - - - - - - - - - - - - - - - - Mantella nigricans 204 - - - - - Mantella aurantiaca 238 - - - - - - - - - Mantidactylus cf femoralis 187 - - - - - Mantidactylus peraccae 272 - - - - - - - - - - Aglyptodactylus madagascariensis 505 - - - - - Laliostoma labrosum 508 - - - - - - - - - - Boophis tephraeomystax 182 - - - - - Boophis albilabris 185 - - - - - - - - - - - - - - - - - - - - - Nanorana pleskei - - - - - - - - - - - - - - - - - Nannophrys ceylonensis - - - - - - - - Euphlyctis cyanophlyctis - - - - - - - - Hoplobatrachus occipitalis 513 - - - - - Hoplobatrachus rugulosus 928 - - - - - - - - - - - Fejervarya kirtisinghei - - - - - Fejervarya syhadrensis - - - - - - - - - - Sphaerotheca breviceps 893 - - - - - Sphaerotheca pluvialis - - - - - - - - - - Fejervarya limnocharis TJ15 - - - - - Fejervarya cancrivorus - - - - - - - - - - - Quasipaa exilispinosa 1030 - - - - - Paa verrucospinosa TJ23 - - - - - - - - - - Limnonectes kuhlii TJ14 - - - - - - - - Limnonectes grunniens 986 - - - - - - - - Limnonectes blythi TJ22 - - - - - - - - Taylorana limborgi - - - - - - - - Limnonectes acanthi - - - - - - - - Limnonectes heinrichi - - - - - Limnonectes visayanus - - - - - - - - - - - - - - - Micrixalus borealis 1020 - - - - - - - - Occidozyga baluensis 930 - - - - - - - - Occidozyga lima 1010 - - - - - Occidozyga laevis TJ12 - - - - - - - - - - - - - - - - - - - - - - Tomopterna delalandii TJ5 - - - - - - - - - - - - - - Afrana fuscigula 590 - - - - - - - - Amietia vertebralis TJ45 - - - - - Afrana angolensis 1014 - - - - - - - - - - Strongylopus grayii 589 - - - - - - - - Cacosternum platys 1045 - - - - - Anhydrophryne rattrayi - - - - - - - - - - - Arthroleptella bicolor 591 - - - - - Natalobatrachus bonebergi - - - - - - - - - - - Pyxicephalus edulis 944 - - - - - - - - Aubria subsigillata 961 - - - - - Aubria subsigillata TJ117 - - - - - - - - - - - - - - - - - Arthroleptides sp TJ62 - - - - - - - - Petropedetes palmipes 841 - - - - - - - - Petropedetes newtoni 965 - - - - - - - - Petropedetes cameronensis 843 - - - - - Petropedetes parkeri - - - - - - - - - - - - Indirana sp1 FB2000a - - - - - Indirana sp2 FB2000b - - - - - - - - - - Conraua goliath 919 - - - - - Conraua robusta TJ113 - - - - - - - - - - - - - - - - - Phrynobatrachus calcaratus 1024 - - - - - - - - Phrynobatrachus dispar 1009 - - - - - Phrynobatrachus mababiensis TJ72 - - - - - - - - - - Dimorphognathus africanus 963 - - - - - - - - Phrynobatrachus auritus 849 - - - - - Phrynobatrachus natalensis TJ61 - - - - - - - - - - - Phrynodon sandersoni 848 - - - - - Phrynobatrachus dendrobates 1015 - - - - - - - - - - - - Micrixalus fuscus - - - - - Micrixalus kottigeharensis - - - - - - - - - - Ingerana baluensis 929 - - - - - - - - Discodeles guppyi 984 - - - - - - - - Ceratobatrachus guentheri 982 - - - - - - - - Batrachylodes vertebralis 994 - - - - - - - - Platymantis pelewensis 896 - - - - - Platymantis weberi 981 - - - - - - - - - - - - - - Ptychadena mascareniensis 181 - - - - - - - - Ptychadena cooperi 588 - - - - - Ptychadena anchietae - - - - - - - - - - - - - - - - - - - - - - - - - - Scotobleps gabonicus TJ130 - - - - - - - - - - - - - - - - - Schoutedenella schubotzi 1021 - - - - - Schoutedenella xenodactyloides TJ79 - - - - - - - - - Arthroleptis variabilis 847 - - - - - Arthroleptis tanneri TJ75 - - - - - - - - - - Schoutedenella sylvatica 844 - - - - - Schoutedenella taeniata 1018 - - - - - - - - - - Cardioglossa leucomystax 845 - - - - - Cardioglossa gratiosa 964 - - - - - - - - - - - Leptodactylodon bicolor TJ129 - - - - - - - - Nyctibates corrugatus TJ126 - - - - - - - - Trichobatrachus robustus TJ111 - - - - - Astylosternus schiotzi TJ116 - - - - - - - - - - - - Leptopelis argenteus 1012 - - - - - - - - Leptopelis bocagei TJ67 - - - - - - - - Leptopelis sp 950 - - - - - Leptopelis vermiculatus 1026 - - - - - - - - - - - - - - - Opisthothylax immaculatus 962 - - - - - - - - - - - Cryptothylax gresshoffi 959 - - - - - - - - - - - Hyperolius tuberilinguis TJ43 - - - - - - - - Hyperolius alticola 1011 - - - - - - - - Nesionixalus thomensis 1017 - - - - - Hyperolius punticulatus TJ35 - - - - - - - - - - - Alexteroon obstetricans 960 - - - - - Alexteroon obstetricans TJ109 - - - - - - - - - - - - - - Tachycnemis seychellensis TJ95 - - - - - - - - Heterixalus sp TJ93 - - - - - Heterixalus tricolor - - - - - - - - - - Afrixalus pygmaeus 1019 - - - - - Afrixalus fornasinii TJ44 - - - - - - - - - - - - Acanthixalus spinosus - - - - - - - - Phlyctimantis leonardi TJ119 - - - - - Kassina senegalensis TJ85 - - - - - - - - - - - - Hemisus marmoratus TJ78 - - - - - - - - Breviceps mossambicus 942 - - - - - - - - Probreviceps macrodactylus TJ69 - - - - - - - - Callulina kisiwamsitu TJ77 - - - - - Callulina kreffti - - - - - - - - - - - - - Kalophrynus pleurostigma 933 - - - - - - - - Synapturanus mirandaribeiroi 530 - - - - - - - - - - - - - - - - - Dyscophus guineti TJ82 - - - - - - - - - - - - - - Liophryne rhododactyla 983 - - - - - - - - Aphantophryne pansa 980 - - - - - - - - Oreophryne brachypus 979 - - - - - Callulops slateri - - - - - - - - - - - Genyophryne thomsoni 993 - - - - - - - - Sphenophryne sp 989 - - - - - Copiula sp 992 - - - - - - - - - - - Cophixalus sphagnicola 990 - - - - - Choerophryne sp 991 - - - - - - - - - - - Scaphiophryne marmorata TJ57 - - - - - - - - Kaloula pulchra TJ41 - - - - - - - - Chaperina fusca 932 - - - - - - - - Calluella guttulata 931 - - - - - - - - Microhyla heymonsi TJ26 - - - - - Microhyla sp TJ70 - - - - - - - - - - - - - - - - - - - - Dasypops schirchi 888 - - - - - - - - Hamptophryne boliviana TJ86 - - - - - - - - Elachistocleis ovalis TJ51 - - - - - - - - Dermatonotus muelleri 1185 - - - - - - - - Gastrophryne olivacea 1053 - - - - - Gastrophryne elegans TJ74 - - - - - - - - - - - - - Ctenophryne geayei TJ27 - - - - - Nelsonophryne aequatorialis - - - - - - - - - - - - - - - - Platypelis sp TJ58 - - - - - Anodonthyla montana - - - - - - - - - Plethodontohyla sp TJ56 - - - - - Stumpffia sp TJ59 - - - - - - - - - - Hoplophryne rogersi TJ68 - - - - - Ramanella obscura - - - - - - - - - - - - Phrynomantis bifasciatus 941 - - - - - Micryletta inornata - - - - - - - - - - - - - - - Heleophryne purcelli 633 - - - - - Heleophryne regis 906 - - - - - - - - - - - - - - - - - - - - - - Brachytarsophrys feae - - - - - - - - Xenophrys major TJ19 - - - - - Xenophrys major - - - - - - - - - - Megophrys nasuta TJ107 - - - - - - - - Ophryophryne poilani TJ21 - - - - - Ophryophryne microstoma TJ36 - - - - - - - - - - - Leptolalax pelodytoides TJ25 - - - - - - - - Leptobrachium chapaense 450 - - - - - Leptobrachium hasselti 1022 - - - 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