diff --git a/tools/ete-toolkit/.shed.yml b/tools/ete-toolkit/.shed.yml new file mode 100644 index 00000000000..dd5ca28187d --- /dev/null +++ b/tools/ete-toolkit/.shed.yml @@ -0,0 +1,11 @@ +name: ete_treeviewer +owner: iuc +categories: + - Phylogenetics +description: A toolkit for the analysis and visualization of trees. +long_description: | + The Environment for Tree Exploration (ETE) is a computational framework that simplifies the + reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit +homepage_url: http://etetoolkit.org +type: unrestricted diff --git a/tools/ete-toolkit/ete-treeviewer.xml b/tools/ete-toolkit/ete-treeviewer.xml new file mode 100644 index 00000000000..f29ecb7b485 --- /dev/null +++ b/tools/ete-toolkit/ete-treeviewer.xml @@ -0,0 +1,149 @@ + + visualize a phylogenetic tree + + 3.1.3 + 0 + + + topic_3293 + + + operation_0567 + + + ete + + + + curl + xmlstarlet + librsvg + + tree.svg +#else + -d "tree=\$(cat '$input_tree');$ncbitaxa" | xml format - > tree.svg +#end if + +#if $output_format == 'png' + && rsvg-convert -o tree.png tree.svg + && mv tree.png '$output_tree_image' +#else + && mv tree.svg '$output_tree_image' +#end if + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/molbev/msw046 + + diff --git a/tools/ete-toolkit/static/images/example-treeview.png b/tools/ete-toolkit/static/images/example-treeview.png new file mode 100644 index 00000000000..7ea93e8eaf4 Binary files /dev/null and b/tools/ete-toolkit/static/images/example-treeview.png differ diff --git a/tools/ete-toolkit/test-data/example-alignment.fa b/tools/ete-toolkit/test-data/example-alignment.fa new file mode 100644 index 00000000000..e457f6b632f --- /dev/null +++ b/tools/ete-toolkit/test-data/example-alignment.fa @@ -0,0 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+-I----------SYNLLE-LDVDKLFEEHKIEEIVEIEKLLDAEIERKRVELRSMVGDRYKDVLAASDAIKNMKTISQQI-VDN--IQNITDICEDLIESKD-DKAAKTL---P--------E--ID--TKCNEERV--LIVQVRLAIFMNEQIWTALDGGDNLTAAQFYLLAQHIHMGLSLTK-----K-EYLDKLPLLKQIRANLATLRDQIFERIKQKLEFVEITAEETSSNLNALLLLRNQSATDLLNIFIEHRKIALNTVINTS--H----ASVRLQISAMVRCLITTIHLLHDCFMCYGNS-------KKGLIWQQLENIVEDESI-PTL----SKVDLPVTPL-IAYIPDVIKQFRPKYKS-FVGESAPENVK--LGEWLASTKESVCKGLESSLKLITSVKGLHIIREEALKIE-----LPSDWERICSESNL-PEN-FNVWYYFFQSLITKRASELISKKVSCIIKDLESEIREVLSGNLGS---------EHGETDLRWYTWVEDPTDVSRI-----E------NKHTGLSMKTLGYSQNVVNLCEKLDGKYLELLIDVSQYLYGKEFTD-----D-VIIYPHLKSDRKKFVDREELENHLRLESTKNSTSLTLFLH-FIK------------SESHKVAKSLLCARFLQAVTNLCPHFNKCC-T------------------------------FNASTEDWSRICGHFTKSSVQFWENWIESCVQETDKQARKLFS-D-VSVCSMISVLLRWDSIEIQEQTDE-KIFKSQIKVPLKPSLTLHRLLSKLNDDLSHVLPHTLPKQVHLQFIEKTTETILNHYKL-------ALD--HNQLNQNQSLQLLFDVKFVTTFSIQRENS------KLVALSQEICDKLRARIDPFDLDVFYSHLQNNVKRAVLQSQAILGCLLPSSAQ--L--AN----LGVGEKFK--EEKEPSVMALSVP---SVSFPLFCTFAHQI--PAQKAPVVDVQEK----------VSS--P-K-------LTK-TTPK--RS----------------DPTA--AI-RSGAAALFGGLTTDWFS---- +>13037.EHJ66433 +-Q----------EQNLLD-IVPDKLFQTHSISEIDNVQKKLQYEIERKREELRAMVGERYRDLIHAADTIEEMLTTTSST-LEH--INDMMATCRNLHDTHL-VGFKINE---K----K-HSQ--NS-QASIDPVHS--ISVQIKLLMEIPEKIWKSLEVNDFVKAAQLFIMARHINTGLQLQIAD-RNTNPGKSLYQLIQQQWNSISHLSDTIVEMCGQKLRDVDISAEVSCSCLIGLYLLDSQSMVELLNTLIDLHSNTLAQILE-DV-K----AQIKKKIINSVKIVMKTVVLVYACFVENQGG----------AVLDKLKDLYRPDSQ-PLI----ELI-QFSDANALKLLPSAITNYRLSLSK-DLSPLAADQVTGSVQRWSVWVKSFILENVTSLLQNITRIRVLHEIREETFKIE-----CPQNWSTMCSSLGI-PE--VHIWCTYFQPLLTARVRNIIETRWQKINDSFKTQILIDLSKVASD----------DREADINWFVWKDLIGDTVIESRNEVVSVME--SLMKGMSRQDRGFTPALQKLCQSLDDELQKLLEDLKDYLYERKDKD---P-------LYDDELDQVYTDKEEIETYLKEASDRNIHSIIQYIRACFDE-T------LQSTELQRKTTAVYTARFTQAITVLMPCLRKCYITLD-------------------------------DTKAWNDICAVLKENCLFCWSKWLDIAEVKI-NELTTGLPQRFTLEDNIDYLMMEWDVMKIEEKDEDGNPVESTIKVPAGPSLKLQEYLYSISRILDEVVPHTLPSEIHARYIDKTISISLAHYNR-------VIRENEQDINQRCALQLLMDVRHLTLLMVARDNK-------AMELSQDICDVLRHKIDPFDYDVFYPYIQTSLKRSVQRVMILLGSTSQPQSL------S----KPVRSGGS--ADSAARILAAADA----PWFSLLPVALPVKKEK----VAKKKP------------STS--P-S-------KTK-PDVT--DNI----------MSASLP-IN-FANARSGAASFFNSMTSDWFSG--- +>34740.HMEL012959-PA +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MMQLLNTLIDLHSNSLAQILDGDV-K----AQIKKKIVNGVKIVMKTVELVFACFVEM------------------LNDLYEIKSP-PLL----ELV-QFSDAAALKLLPSGVTTY-------------------SVQTWSVWVQSFINDNVQALLQNITRVKALHEIREETFKIE-----SPPKWSIICNSLDI-PA--VHVWCHYFQPLLTSRVKLIIDNRWQRVYDTFKTQLLVDLTKKLLE--------------DLKDYLYQEKKK--------------------------------------------------------------D-------IIVFDDEDSVEQVYIDREIVEEYLRNTSDKNILNMINYIKACFEE-S------LQTTELQKKTLCIYTARFLQAITTLMPNLHKCYINEVT-------------------------SMNDNAIKSWNEMGVVLKENCQFCWIKWLDIVEEK-----------------------IQWDIIKIEEKDEEGKSIESTIKVPCGPSLKLQEYLYSISRILDEVIPHTLPTEIHSMFIERTIAISFAHYNK-------VIRMKEMDITQRCALQLLMDVRHLTLLMVARENK------KSIELSQDICEFLRQKIDPFDYDVFYPYIQTNLKRSVQRVQTLLGSLILHHGQLTGIIGN----KPILSGGS--GDKTASLLASADT----HWFSILPVATPNVNKK-QDKMVKKKP------------QSS--P-N-------KSK-SDI---TDI----------MSNSLP-IN-FANARSGAASFFNSISTDWFRLN-- +>7091.BGIBMGA012450-TA 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+>6669.DappuP312785 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+>7425.NV10250-PA +-S----------TDKFLD-LDIRKLFEEHGIKDIELIQKQIQHESDRKKIELRTLVGERYRDLIQAADSIAQMKQTSESV-VAK--IVNIEKTFHDLQQKYL-IGFKMHT---E----HV-HS--QR--APNQISDS--VVMQIKILMDIPEQIWSAIDSKDFLLATQLFLLAQHINYSLKFEIG----DANLASRYPIVSKQWGIINQFKSLIFNFCNDALQSVHLSKELAANCLAALVLLDGLNSADLLNRLISLRSQTIKSIVISES-D----LSVKNKIKLCLNVLMDTIPLISSCFIKYRDS-------QDGLVSMYINEIKDTNAF-LML----SQL-DLEEELIQKFLPLVAKNHKPFVQH-ELKKLPLANVQESVNAWFNWVKQLATIEVTKLLNLITSVKGIYSIREECLAVE-----IPENWDSTWDAFSL-PS--VNFWTEFFQPLLTARVKGILSDKLDVCLVNLKKDVSELLGKVSFET-------AQYPENDLRWFVWKDSPEDIPQKLMEGGTL-----DSKRPLLLKARAFSPNVVKLCENFENNLSEVLLHLKQYLYELEQTS----MKDDLLAADIYLTSNKFCDRTEIQEYLQSVSGKLIDDFVVFVKECIIE---------KPKSGRQEVNAIVTARFLQAIPSMCSNFKECFTISRP----------TG---------------ITLTNMKWQEVCDKLKQESTLAWSVWAKCFTKVIHYNRNKYLIKETADELRNHTIITDWEKVIIEEEAEEGKRINSEILVPYQPAVHLQKFLAFVCQDLNKVIPHTIPKSILNVLINNVAVELFNYYYG-------LST--SLDIRQKQAIQILFDVKYISLLMVPRDNK------LLVEQSNKVCNSVISKIDPFDFDVFYPFINTNVKKGVQRSLLIFGNLVPHMEQLHSVLGA----RIEHSDGFKSIKDPPGVLALCSG---TPWFPPLAVTAPTKSLPVIQLPVPERPQ---------------------------------R--RKQ-HP------SKEHTRS-TG--STIKSGAAAFFGAMGSDWFSTS-- +>7460.GB18353-PA +-T----------TTNYLD-LDINKLFEEYTIKEIEAIQKKIQHESDRKKIELRTLVGERYRDLILAADTIRKMKITSEHV-ISR--IIDIENKFGELQKKYL-IGFKIDS---I----QN-DD--EK--NVEASQDS--IIIQIKILMDVPQYIWSSIENKDLLFATQLYLIAQHINYSLLFEVG----STDLSIKYPIVSKQWDVISQFKNIILNKCNNVLQSLDVQPGSIANCLAAFVLLNGTSFSDLLDKLISMRNQAIKSIVTDEN-D----NSVKTKIKL-----------------YSEGE-------SGGLILQYLIKIQDQEAY-SLL----SQL-DLNQELLQEFLPLVTKQHKPFTVH-NSENFCILDLQKRIKSWLHWVAEFCNHEITKLLDLIISIRGLYYVREEAVNIN-----LPENWNKIWEELSL-PR--ITFWVEFFQPLISQRVK--------------------------------------------------------------------------------------------------------HLEQYLYETERVM----IKDNLLSTNISLISDSFFDRAEIQEYLQTISTNMIEDFINFAKTCVND---------KPDYGQRDVNAIVMARFLLALITLSSNLNKCFTLSKV----------SG---------------LTITNMKWQTICDKLKEESTFIWSVWAKTYKVKISEHREKFISKESLHGYPIHLVISEWEKVTIEEDSGEGKRIKSEILVPYQPSIHLQKFLTAINKDLNKIIPHTLPKKVLHEVIEDVVTELLNHIIV-------FN---DANLSQKQAFQVLFDIKYSSLLMIPRENK------ILIDLSNKSCETILSKIDPFDYDVFNPFIHTNVKKSVQRSLLILGNLIPHLEQLHSILGA----RSEYNNIEGVKSDLPTVLALYTG---APWFPPLTVTAPAKNLPLVTATLPEKTQ---------------------------------N--HIF--------------------------------LISK--IYY---- +>12957.ACEP_00009457-PA +-T----------TTNYLD-LNINKLFEQHTIKEIEEIQKKIQLESDRKKLELRTLVGERYRDLILAADTIGKMKITSEKV-TSR--IINIEDKFRELQKKYL-IGFKTEP---I----ED--K--LD--KKGYIFDS--VIIQIKILMDIPQYIWTSIENQNLLFATQLYIIAQHINYSLMFEVG----STELSRRYPIVSKQWDVIMQFKNIISNECNKILQSLDVSTINAANCLASLVFLNESSFADLLEKLISTRCMAIESVIKGEG-H----DSVKNKLKSCMKILIQTVHLIYSCFINADNA-------PGGLVLQFVADIKDQEAY-SLL----SQL-DLDQDLLQEFLPSVTKHHKPFVQD-IPKTFSLPALQNSVKSWLEWVNNFSNLEITKLLDLIVSIKGLYNVREEAISIN-----LPENWNSIWEELSL-PR--ISFWIEFFQPIITRRAKCIITNKWTDALADLKSDITELLDKIAHDK-------FEFPEHDLRWFVWKDSPTDIPQKLTKNGGL-----DNKRSLLMKAKGYSPNVIKLCEKFDENLYALLSDLEHYLYETERVI----IKDSLLSANISLIANSFSDRNEVQEHLQVISTEKIEDLVQFIKTCVND---------KPKHGQSDINAIVLARFLFALTTLCSNLNKCFTSSKV----------SG---------------LIITNVKWQAVCDNLKEESTCMWSIWANIYKVKISEHMKKYILKEPIDGLRVHWIVSEWEKITIEEESGEGKRIKSEILIPYQPSIPLQKFLTAICKDLNKIIPHTLPKRVLQQIIESIITELFNYYLN-------ASK--NIDLRQKQAFQVLYDIRYCTLLMVPHENK------ILNELSTKTCDAVLAKIDPFDYDVFNPFIHTNVKKSVQRSLLIFGNLVSHLEQLHSILGA----RNEHTSNE--RTEPPAVLAVCTG---APWFPPLTVTAPTRNLPLLSMPVPDKTQ---------------------------------K--KIT-K---------EHVKE-PT--SAIKSGAAAFFGAMGSDWFGSSN- +>51511.ENSCSAVP00000011400 +------------------------VFERNNVEEIRELEKKTRHEIELKKEELRQMVGERYRDLLEAADKITGMKKYSEI-VTST--IKDIQEYKRTLS--V----------P--KLR---AS--QLSV-KNENRFL--ELAAETKVLMEMPEEIWLQVEAGNMITASFLYLQSLQVLKNLSLEGN--HSYSPILQWIPMLGQQAQAVGNLRSAILKQCNTRIADHALDLQSISEALCSIVLLEDVSIRCVLTKLLEARRYAIREILTATKNH-G--MGTKGKICASLDILVKTTSQVFELFCSHPQSK--G------VVETMLQKCTQ------EP-D--NSD-NCTK-IWSNCVPKNLALQKVKFN-ITDFTIPEEIIQQLNTEWLTGCKSDLTEGIADLLKFTNSAKDLTNVRIAVMDILDQNPT-KTKWQNTCQAV-FKQ--EVIVWNEILEPLFLNKMKLVVSNTFDELLSESKVMLEQ-----Q----------HHGKGTSISTFLWQEHENDIPSTMAWQGWQHRKT-SENPGLTLKSLAITPNVHQLCELLNKTVRKLLDDVNNYMLSVVAKDKTD---YKR--TASETKVETNQECLTVFSYLKQSSGNFFDSLSQLLSSLEQQLKSKVSKTDYSANEPVLSKALFLSQVCRNFFKLCHTFKECYVTNYTTNQPVR-RHL---SESHSAGDVK----TTTDSSAWDDVVHSMSQQSLNLMTLCCNAILYPAIAAYKVSLLDS--ASGNILLSLSQWDCITVEEESESGNTVKSKIRVPASTMSFTQELLFTVCTEIEKIGGYSISRLTLRNLSSRCLQSILEAFSAAAFARNISDDD-TRSPSQVWALQCLFDLRYLHHLLYQP---LPNEDHENSFTYTELVDWLEGYIDPFDLDVFSPHITNNIQLYAARTSTLFGILVVSNK------TSSQK----L--FS--SKDSHNVLPLM--------------------------------------------------------------------------------------------------------------------- +>7719.ENSCINP00000035803 +V-AVIPITYKYL---IITMDSVMTIFERNGVEEIRELEKKTRHEIELKKEELRQMVGERYRDLIEAADKITEMKKCSEI-VTNT--VKDIQEFTSARRKSA----------L--KPR---AS--QLGA-SNESRFL--EIAAETKVLMEMPEEIWLQVEAGNMITASFLYLQSRQVLKNLSLDGN--HSYSPILQWIPMLGQQAQAVANLRLAILKQCHARIRDHSLDLQSLSEALCSIILLEEVSIETALGKLLESRREAINEILTEAEYY-G--MSTKGKICAGLEVLVKTASQVYELFCCEGERK--S--AVEIMLRKCTEEPEGT-----EPSESFGLG-KCFK-IWTSCVPKNLSLQKVKFN-ITSYNIEDKNIQQLNTQWLSACKSILNKGIADLLQFTNSAKDLTSVREAAMEILDCGHV-KTKWQQTCQAV-FNH--EVDVWDELLQSLFLNKLKSIVAVTFQQLLNDSKALLEK-----Q----------GGEKGTSTSKFLWNEHENDISSTMAWSSWQQRKT-SDHAGLTLKSLSITPNVHRLCEGLDTSVKKLLDDVNNYVVSVVGKSGPN---HKRSVSTSENLIENNVECQTVYGYLKLSSGEFFTSLLEFLSKMKEQLKNKANKTDYTANEDVLSKALFLSRVCRNLFKLCHSFHDCYITKPLHNQPLR-RHM---SESHASGDMK----STTDTSQWEAIVEAMSVQSLNFMSICTNAILSPALVSFEESLLNS--ASGNILLSLSLWDSITVEEESETGDTVKSQIKVPASTMSFTQELLFTVCTELEKIGGYSISRSTLRELSNSCLQGVMRAYSSAALARTLPEED-AS-PSQVWALQSLFDLRYLHNILQQSNPEVGEDEEHPCFTYTELVDWLEGYIDPFDLDVFSPHLTHNIQRYSARTSTLFGILVSS-K------TSSQK----L--FS--SKDSHNVLPL---------------------------------------------------------------------------------------------------------------------- +>10228.TriadP54105 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+>7739.JGI126010 +-----AAEMKPE---HIATMDTNILFQKYTINEVKDTEKRVR---------------ERYRDLIEAADTIREMKNS-NNV-GQA-V-SSMDKYCQQLQ-KNKKNH-------A--REN--ME-A---A-KEHDAF--YSIAAEIKLLLDMPEKIWSSLEADELLSAARLYLLSRHIITSLHLDSPSPPSTQSLLTFFPILSRQWSYISHFKVAILK------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HR---DISAGGDSSTDPPPFDKFADNIHLEKYLQNGCTSCIT------------------------------RALFLARLCAGLVEICPNLQLCMMGKQLKDGTQD--SA---RVLHKQGSSK-MMPPLDENSPWGKLRSQLFATADIGHRLWAEHTSGWLVDQFSSALKDS--SPAALLMSATNWEEMEIQEETEAGKSVQSKIRLPAQASWYVQSMLFLLCREVNRVGGHALSRSVIHEVVQQTCAGVLTAYEALL-------QD-SATLPQARALQLVFDLRYITNMLSARGPDSQAY-RAQADRVMRLLEKIENHIDPFDLDVFTPHLSKALDRLTQRCSVMLGVTTSPDRH----LAAGRP----PGSTG--QQEQHNVLPLPPP---IPKFTLLPITTRT----------------DSKPRQTIEV--PVP-K-VQ-VLPSLSSS-GSRDV--ED----SGRLP---R--A-ASP-SSLYSIGAFST----GWLSNIGQ +>7739.JGI126021 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+>6085.XP_002167371 +-------M--VS---LP---DVRLLFQTHSIEEINVIEKKIRGEIEKKKDDLRIMVGERYRDLINAADTIKDMESESSQ-VFGG--IKNIQNLCLSFHTSL-MSSCSS---K-------------TQS-PRDVAFY--SLATQMDLLVNTPEKIWNALDNHEYLNATQLYMFSHHIVNILVNDPK-P-NSQDVYASFPVLHHQWAAISHFKTSILKGAEYSLKDKTLPDKKLCESLCSLALLDNCSPRQVFATLLLARK-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>7757.ENSPMAP00000006833 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGLTMKARGHTPMVQGLCAALDAKLRARIEDVAAYLPPAGPPAS---G-QAPLPQQDSAGFDRFADSGRVQETLQKESASCITALSACARGHLDASAQEGGGGDDEQRRHHLAIVLFVARLCRAIPELCPSLRLAILGAAGVTSPPEAVRP---LPRALAGEAR-SVPRGGRTTAWTELSEELGALSLRAYDAWSRNVAQVAVSEFGSTLRVE--SPGRVLGSTPNWEEIEIMEETESGGSVASKIHLPAQAQNAAQALLFGLGQAMGAVGAQAVPRVTRQALLEAVMDGVLTAYEARLQPAHARTAG-TTPMCQARALQLLFDLRFMHGVLAVRPEGTRGSSAAALCRIQAVVDDLESHVDPFDLDVFTPHLHLHLQRLLQRTNVLFGVLTGTERQ----HTGRPA----P--S---GPEAPSLLAMAAT---HARFALLPLPASS----------------LASQRRATPP--V-------RRGPATAQA-PGVDT--RP----PGALF---R--QLASH-DEGSQGSSLFKL---GWLSAITK +>7668.SPU_016633tr +----------MS---IADL-STNQLFEKYTIEEIRKLEKDTRDEIETKKEDLRQMVGERYRDLIEAADTITEMKTCSEK-IFQS--IQDMQKHCVNLQKTH-LTKGIS---L--SPK---KA--ASSR-SQSSGFY--AIASQTKLLLDIPEKIWSDIESGEHLHATQLYLLACHIVSSLQLDTT-THQSTQLLKWFPVLSRQWAAICHFKPSILQSCRNVLKNATASDMVITKALCSIMLLEDTSPRQVFTEFLLARKNAVHQAFSSSQ-F-D--ASVKKQVCGVTNLINLTLRQIHAIFYHQEGDE--NNDEEGNLLQKVLTEATSS----SDGKTVLADE-LAVG-TFSKHLPANITDFHPTLR-SSTDPIAAPYLQECVSQWVETCISDVHDGISKLLNYVTSIRGLTSIRDAVWDLLQED-D-VPALRNITKRV-LGR--SLCLWGEFVRPLFLSRMQAILQDALDQTLTNSHQLVIQASHDMESSP----------ADLDVAAHTWKEMSSDLPSPMAWRGGAGSRD-LDAGSLYMKARAFTPKTQSICSFIDVRLKSLLEDLSSYTDRQTDKQPSD---QKSASKSSQEPFDKFADTVNLHSFLQIACTKCVSRLADHIKEELSDCKLAQEEKLEDQSSVIINRVVFLGRLCSALTELSPHLQQAVLITEKKDSKG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DPL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>7668.SPU_013365tr +----------MS---IADL-STNQLFEKYTIEEIRKLEKDTRDEIETKKEDLRQMVGERYRDLIEAADTITEMKTCSEK-IFQS--IQDMQKHCVNLQKTH-LTKGIS---L--SPK---KA--ASSR-SQSSGFY--AIASQTKLLLDIPEKIWSDIESGEHLHATQLYLLACHIVSSLQLDTT-THQSTQLLKWFPVLSRQWAAICHFKPSILQSCRNVLKNATASDMVITKALCSIMLLEDTSPRQVFTEFLLARKVRSNDCLAPRL-T--------------------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHYQ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- diff --git a/tools/ete-toolkit/test-data/example-tree-ncbi.tree b/tools/ete-toolkit/test-data/example-tree-ncbi.tree new file mode 100644 index 00000000000..9a9dce81bb7 --- /dev/null +++ b/tools/ete-toolkit/test-data/example-tree-ncbi.tree @@ -0,0 +1,2 @@ +((6669.DappuP312785:1.24473,(((7739.JGI126010:4.02e-06,7739.JGI126021:0.168081)0.99985:0.848895,((45351.NEMVEDRAFT_v1g217973-PA:1.49614,(6085.XP_002167371:1.08059,10228.TriadP54105:1.08509)0.457684:0.128729)0.99985:0.321915,(7668.SPU_016633tr:0.00222941,7668.SPU_013365tr:0.093091)0.99985:0.642533)0.888302:0.101463)0.998565:0.12537,((51511.ENSCSAVP00000011400:0.259936,7719.ENSCINP00000035803:0.209259)0.99985:1.762,(7757.ENSPMAP00000006833:0.945887,((7955.ENSDARP00000103018:0.187989,(8049.ENSGMOP00000003903:0.283082,((8128.ENSONIP00000009923:0.172432,(69293.ENSGACP00000005927:0.11289,(99883.ENSTNIP00000008530:0.0637802,31033.ENSTRUP00000029741:0.0851327)0.99985:0.111539)0.750558:0.0140823)0.99985:0.0210439,(8083.ENSXMAP00000007211:0.156672,8090.ENSORLP00000021771:0.242897)0.99985:0.0332475)0.99985:0.0502247)0.99985:0.097906)0.99985:0.204816,(7897.ENSLACP00000021045:0.20103,(8364.ENSXETP00000053091:0.389689,((9258.ENSOANP00000015194:0.652603,((13616.ENSMODP00000032296:0.0669026,(9315.ENSMEUP00000005072:0.0368095,9305.ENSSHAP00000018667:0.0280404)0.997706:0.0140274)0.99985:0.109803,((9361.ENSDNOP00000011178:0.093465,(9371.ENSETEP00000005953:0.276816,(9813.ENSPCAP00000009886:0.0800451,9785.ENSLAFP00000023898:0.0550027)0.99697:0.0294647)0.99985:0.0375967)0.608183:0.00574174,((((30608.ENSMICP00000006810:0.0353003,30611.ENSOGAP00000013460:0.0515798)0.99985:0.034051,(9478.ENSTSYP00000011163:0.0656837,(9483.ENSCJAP00000037059:0.0556713,(9544.ENSMMUP00000001688:0.00821597,(61853.ENSNLEP00000001585:0.00543935,(9601.ENSPPYP00000009641:0.00544861,(9593.ENSGGOP00000014253:0.00241737,(9606.ENSP00000299886:0.00108745,9598.ENSPTRP00000016297:0.00216932)0.993995:0.00108247)0.99985:0.00217395)0.99985:0.00216928)0.99985:0.00380297)0.99985:0.00880979)0.99985:0.0259329)0.993631:0.00725957)0.99985:0.00775695,((((10141.ENSCPOP00000018381:0.0312261,10141.ENSCPOP00000003239:0.0560276)0.99985:0.131426,(10090.ENSMUSP00000018805:0.0326181,10116.ENSRNOP00000003804:0.0330137)0.99985:0.081468)0.995671:0.0105266,(43179.ENSSTOP00000001636:0.0584822,10020.ENSDORP00000002346:0.148367)0.976029:0.00712029)0.99985:0.020967,(9986.ENSOCUP00000010215:0.342444,37347.ENSTBEP00000010812:0.0710806)0.981559:0.0148504)0.99985:0.0111655)0.99985:0.0141806,((9823.ENSSSCP00000018275:0.0497089,(9739.ENSTTRP00000004916:0.0624029,9913.ENSBTAP00000007999:0.0933538)0.99985:0.0153799)0.99985:0.0353429,((9796.ENSECAP00000006507:0.0593149,(9685.ENSFCAP00000004377:0.0895056,(9615.ENSCAFP00000006718:0.0344248,(9646.ENSAMEP00000002816:0.0246918,9669.ENSMPUP00000014182:0.157245)0.979337:0.0106908)0.990824:0.00781435)0.99985:0.0209773)0.99291:0.00461526,(59463.ENSMLUP00000015199:0.175449,132908.ENSPVAP00000006353:0.0636063)0.828177:0.00861023)0.805512:0.00313751)0.99985:0.0138134)0.99985:0.0180555)0.99985:0.0925821)0.99985:0.0504324)0.99985:0.0408666,(28377.ENSACAP00000014302:0.2972,(13735.ENSPSIP00000020553:0.125656,(59729.ENSTGUP00000002997:0.21101,(9103.ENSMGAP00000006649:0.034221,9031.ENSGALP00000007041:0.0301602)0.99985:0.14558)0.99985:0.0950631)0.912514:0.0193477)0.99985:0.0543705)0.99985:0.0558399)0.99985:0.0851946)0.996306:0.0767894)0.99985:0.242292)0.99843:0.214734)0.760404:0.170331)0.99985:0.889243)0.99985:0.309174,((7070.TC009561-PA:1.414,(7029.ACYPI001869-PA:2.67503,((34740.HMEL012959-PA:0.216556,(13037.EHJ66433:0.30242,7091.BGIBMGA012450-TA:0.234676)0.691542:0.0356537)0.99985:1.06833,(7425.NV10250-PA:0.448078,(7460.GB18353-PA:0.265179,12957.ACEP_00009457-PA:0.219522)0.99985:0.223062)0.99985:0.715703)0.950323:0.0960579)0.630765:0.0828761)0.868488:0.104171,(121225.PHUM413450-PA:1.38201,(((43151.ADAR004533-PA:0.286189,7165.AGAP001322-PA:0.216522)0.99985:0.404262,(7176.CPIJ007948-PA:0.310705,7159.AAEL007141-PA:0.261808)0.99985:0.238196)0.99985:0.352684,(7260.FBpp0240708:0.24283,((7222.FBpp0149372:0.191481,7244.FBpp0224481:0.114954)0.99985:0.156407,(7237.FBpp0281462:0.118908,(7217.FBpp0120932:0.132407,(7245.FBpp0269552:0.0320153,7227.FBpp0082093:0.0340969)0.99985:0.0854297)0.99985:0.0800303)0.99985:0.0655239)0.825983:0.0710402)0.99985:1.14395)0.99985:0.708932)0.628915:0.0819834)0.99985:0.309174); + diff --git a/tools/ete-toolkit/test-data/minimal-tree-out.svg b/tools/ete-toolkit/test-data/minimal-tree-out.svg new file mode 100644 index 00000000000..e012f94feb9 --- /dev/null +++ b/tools/ete-toolkit/test-data/minimal-tree-out.svg @@ -0,0 +1,476 @@ + + + Generated with ETE http://ete.cgenomics.org + Generated with ETE http://ete.cgenomics.org + + + + + + + + + + 1 + + + + + + + + + 19 + + + + + + + + + + + + CHLRE_Cre09.g393654.t1.1 + + + + + + 64 + + + + + + + + + VOLCA_Vocar.0001s1384.1.p + + + + + + 71 + + + + + + + + + GONPE_KXZ41109.1 + + + + + + CHLRE_Cre01.g010750.t1.2 + + + + + + 6 + + + + + + + + + 12 + + + + + + + + + + + + VOLCA_Vocar.0020s0165.1.p + + + + + + 17 + + + + + + + + + + + + 51 + + + + + + + + + VOLCA_Vocar.0003s0509.1.p + + + + + + CHLRE_Cre09.g393284.t1.1 + + + + + + 28 + + + + + + + + + + + + VOLCA_Vocar.0008s0105.1.p + + + + + + VOLCA_Vocar.0003s0512.1.p + + + + + + 14 + + + + + + + + + + + + 24 + + + + + + + + + + + + VOLCA_Vocar.0021s0041.1.p + + + + + + 53 + + + + + + + + + VOLCA_Vocar.0021s0042.1.p + + + + + + VOLCA_Vocar.0021s0043.1.p + + + + + + 23 + + + + + + + + + + + + 47 + + + + + + + + + 72 + + + + + + + + + GONPE_KXZ50986.1 + + + + + + CHLRE_Cre17.g738632.t1.2 + + + + + + VOLCA_Vocar.0026s0121.1.p + + + + + + CHLRE_Cre17.g709800.t1.2 + + + + + + 9 + + + + + + + + + + + + 16 + + + + + + + + + + + + 35 + + + + + + + + + + + + CHLRE_Cre06.g302150.t1.1 + + + + + + 96 + + + + + + + + + CHLRE_Cre15.g643700.t1.1 + + + + + + CHLRE_Cre17.g738600.t1.1 + + + + + + CHLRE_Cre06.g304250.t1.1 + + + + + + 49 + + + + + + + + + 51 + + + + + + + + + + + + 74 + + + + + + + + + VOLCA_Vocar.0024s0053.1.p + + + + + + 18 + + + + + + + + + + + + 47 + + + + + + + + + 79 + + + + + + + + + GONPE_KXZ51696.1 + + + + + + GONPE_KXZ51697.1 + + + + + + GONPE_KXZ54016.1 + + + + + + VOLCA_Vocar.0024s0052.1.p + + + + + + 56 + + + + + + + + + CHLRE_Cre14.g617151.t1.2 + + + + + + CHLRE_Cre14.g617200.t1.1 + + + + + + CHLRE_Cre10.g418600.t1.1 + + + + + + + + + + + + + + + 0.07 + + + + + + + + + + + + 0.07 + + + diff --git a/tools/ete-toolkit/test-data/quicktree_VARL_NCBI.svg b/tools/ete-toolkit/test-data/quicktree_VARL_NCBI.svg new file mode 100644 index 00000000000..4a767bd6e89 --- /dev/null +++ b/tools/ete-toolkit/test-data/quicktree_VARL_NCBI.svg @@ -0,0 +1,1736 @@ + + + Generated with ETE http://ete.cgenomics.org + Generated with ETE http://ete.cgenomics.org + + + + + + + + + + 1 + + + + + + + + + 19 + + + + + + + + + + + + Chlamydomonas reinhardtii + + + (3055.CHLRE_Cre09.g393654.t1.1) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + + + + chlamydomonadales + + + + + + chlamydomonadaceae + + + + + + chlamydomonas + + + 64 + + + + + + + + + Volvox carteri + + + (3067.VOLCA_Vocar.0001s1384.1.p) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + + + + chlamydomonadales + + + + + + volvocaceae + + + + + + volvox + + + 71 + + + + + + + + + Gonium pectorale + + + (33097.GONPE_KXZ41109.1) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + + + + chlamydomonadales + + + + + + volvocaceae + + + + + + gonium + + + Chlamydomonas reinhardtii + + + (3055.CHLRE_Cre01.g010750.t1.2) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + + + + chlamydomonadales + + + + + + chlamydomonadaceae + + + + + + chlamydomonas + + + 6 + + + + + + + + + 12 + + + + + + + + + + + + Volvox carteri + + + (3067.VOLCA_Vocar.0020s0165.1.p) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + + + + chlamydomonadales + + + + + + volvocaceae + + + + + + volvox + + + 17 + + + + + + + + + + + + 51 + + + + + + + + + Volvox carteri + + + (3067.VOLCA_Vocar.0003s0509.1.p) + + + + + + + + + eukaryota + + + + + + viridiplantae + + + + + + chlorophyta + + + + + + chlorophyceae + + + 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