#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 September 19, 2025; 6:43 GMT TreeBASE (cc) 1994-2008 Study reference: Susko E., Field C., Blouin C., & Roger A. 2003. Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models. Systematic Biology, 52(5): 594-603. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1019] [ The following blocks are input data for analysis step 1774 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1774; DIMENSIONS NTAX=22; TAXLABELS Cercomonas_sp. Chlorarachnion_sp. Cyanophora_paradoxa Euglena_gracilis Guillardia_theta Jakoba_incarcerata Jakoba_libera Macropharyngomonas_halophila Malawimonas_jakobiformis Naegleria_gruberi Pisum_sativum Plaesiobystra_sp. Pythium_ultimum Reclinomonas_americana Soginia_sp. Stylonychia_lemnae Toxoplasma_gondii Trimastix_marina Trimastix_pyriformis_pyriformis Trimastix_pyriformis_sulcatus Trypanosoma_brucei Volvox_carteri ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M609] TITLE 'Eukaryotic beta-tubulin'; LINK TAXA = TaxaForAnalysisStep1774; DIMENSIONS NCHAR=431; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Cercomonas_sp. --------------IGAKFWEVISDEHGIDPTGTYRGDSDLQLERINVYFNEATGGRYVPRAILMDLEPGTMDSVRAGPYGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELIDSVLDVVRKESESCDCLQGFQITHSLGGGTGSGMGTLLISKIREEYPDRMMCTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMVIDNEASYDICFRTLKLTTPTYGDLNHLVSASMSGITCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCASDPRHGRYLTAAAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMAVTFVGNSTSIQEMFKRVSEQFTLMFRRKAFLHWYTGEG------------------------------ Chlorarachnion_sp. --------------IGSKFWEVVSDEHGVDPTGSYQGESDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLVSKIREEYPDRMMCTFSVFPSPKVSDTVVEPYNAVLSFHQLVENSDECFGLDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSGVTCCLRFPGQLNADLRKLAVNLIPFPRLHFFITGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCASDPRHGRYLTAAAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSAVCDIPPKGLKMSTTFVGNSTCIQEMFQRVSAQFTMMFRRKAFLHWYTGEG------------------------------ Cyanophora_paradoxa REIVHVQGGQCGNQIGAKFWEVISDEHGVDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAVLMDLEPGTMDSVRAGPYGQLFRPDNFIFGQSGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSMGGGTGSGMGTLLIAKVREEYPDRMMCTYSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMVIDNEALYDICFRTLKLTTPTYGDLNHLVSACISGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFVPLTSRGSQQYRALTVPELTQQMFDAKNMMCAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKASVCDIPPKGLKMSATFIGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEE Euglena_gracilis REIVHIQAGQCGNQIGSKFWEVISDEQGVDPP-DIPGDSDLQLERINVYYNEATGGRYVP-AILMDLEPGTMDSVRAGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGPELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMMTFSVIPSPKVSDTVVEPYNTTLSVHQLVENADEVMCIGNEALYDICLPTLKLTTPTFG-HETLVSAVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLVGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAASDPAHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMSATFIGNNTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATVEE Guillardia_theta --------------IGAKFWEVISDEHGVDPTGTYHGDSDLQLERINVYFNEATGGRYVPRAVLMDLEPGTMDSVRAGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQISHSLGGGTGAGMGTLLISKIREEYPDRIMLTFSIVPSPKVSDTVVEPYNATLSVHQLVENADECFCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCSLRFPGQLNSDLRKLAVNIVPFPRLHFFMVGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCAADPRHGRYLTAAAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKASVCDIPPKGLKMAVNFIGNSTAIQEMFKRVSEQFTGMFRRKAFLHWYTGEG------------------------------ Jakoba_incarcerata --------------IGAKFWEVISDEHGIDPTGTYRGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQISHSLGGGTGSGMGTLLISKIREEYPDRMMMTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCSLRFPGQLNADLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAAADPRHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMAVNFVGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Jakoba_libera --------------IGAKFWEVISDEHGVDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAVLMDLEPGTMDSVRAGPYGQLFCPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMLTFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNVKSSVCDIPPKGLKMAVTFIGNSTAIQELFKHVSEQFTAMFRRKAFLHWYTGEG------------------------------ Macropharyngomonas_halophila --------------IGSKFWEVISDEHGIDPTGAYDGDSDLQLERINVYYNEATGGRYVPRSILMDLEPGTMDSVRAGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMLSTFSVFPSPKVSDTVVEPYNATLSIHQLVENSDEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSVVMSGVTCCLRFPGQLNSDLRKLAVNLVPFPRLHFFMIGFAPLTSRGSQQYRALSVPELTQQMFDAKNMMAASDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFIEWIPNNIKSSVCDIPPRGLKMSSAFIGNSTAIQEMFKRVNEQFSSMFRRKAFLHWYTGEG------------------------------ Malawimonas_jakobiformis --------------IGAKFWEVISDEHGVDPTGAYHGDSDLQLERINVYFNEATGGKYVPRAVLVDLEPGTMDSVRAGPFGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQICHSLGGGTGSGMGTLLIAKIREEYPDRMMCTFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVFCIDNEALYDICFRTLKLTTPTYGDLNHLVSAVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMVGFAPLTSRGSQQYRALTVPELVQQMFDAKNMMAASDPRHGRYLTAAAVFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNVKAAVCDIPPKGLKMSVTFVGNCTAIQELFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Naegleria_gruberi REIVHIQAGQCGNQIGAKFWEVISDEHGVDPTGAYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMMTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSIVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAASDPRHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPRGLKMAATFIGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEE Pisum_sativum RQILHIQGGQCGNQIGAKFWEVVCAEHGIDPTGRYTGDSDLQLERIDVYYNEASGGRFVPRAVLMDLEPGTMDSIRSGPYGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELIDSVLDVVRKEAENCDCLQGFQVCHSLGGGTGSGMGTLLISKIREEYPDRMMLTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMVLDNEALYDICFRILKLSNPSFGDLNHLISATMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMVGFAPLTSRGSQQYRTLSVPELTQQMWDAKNMMCAADPRHGRYLTASAMFRGKMSTKEVDEQMMNVQNKNSSYFVEWIPNNVKSTVCDIPPTGLKMASTFIGNSTSIQEMFRRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVAEYQQYQDATAD- Plaesiobystra_sp. --------------IGAKFWEVISDEHGVDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMMTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLIGFAPLTSRGSQQYRALTVPELTQQMFDTKNMMAASDPRHGRYLTATAMFRGRLSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMAATFIGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Pythium_ultimum RELVHIQGGQCGNQIGAKFWEVISDEHGVDPTGSYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQPGAGNNWAKGHYTEGAELIDSVLDVARKEAESCDCLQGFQITHSLGGGTGSGMGTLLISKIREEYPDRIMCTYSVCPSPKVSDTVVEPYNATLSVHQLVENADEVMCLDNEALYDICFRTLKLTTPTYGDLNHLVCAAMSGITTCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQQFDAKNMMCAADPRHGRYLTAACMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKASVCDIPPKGLKMSTTFVGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEE Reclinomonas_americana --------------IGAKFWEVISDEHGVDPTGTYHGDSDLQLERINVYFNEATGGRYVPRAVLMDLEPGTMDSVRAGPYGQLFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMLTFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNVKSSVCDIPPKGLKMAVTFIGNSTAIQELFKRVSEQFTATFRRKAFLHWYTGEG------------------------------ Soginia_sp. --------------IGSKFWEVIADEHGVDPTGTYHGDSDLQLERINVYFNEAAGGRYVPRAVLMDLEPGTMDSVRAGPYGQMFRPDNFIFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLISKIREEYPDRMMMTFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVMSGVTCCLRFPGQLNSDLRKVAVNLIPFPRLHFFLIGFAPLTSRGSQKYRHLTVPELTQQMFDAKNMMAASDPRHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLRMAATFVGNSTAIQEMFKRVSEQFTVMFRRKAILHWYTGEG------------------------------ Stylonychia_lemnae REIVHIQGGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAVLMDLEPGTMDSVRAGPFGQLFRPDNFVFGQSGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRIMATFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTYGDLNHLVSAGISGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMTGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCASDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMAVTFLGNSTAIQEMFKRVGEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAED Toxoplasma_gondii REIVHVQGGQCGNQIGAKFWEVISDEHGIDPTGTYCGDSDLQLERINVFYNEATGGRFVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRIMETFSVFPSPKVSDTVVEPYNATLSVHQLVENADEVQVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSGVTCCLRFPGQLNSDLRKLAVNLVPFPRLHFFLIGFAPLTSRGSQQYRALSVPELTQQMFDAKNMMCASDPRHGRYLTASAMFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNMKSSVCDIPPKGLKMSVTFVGNSTAIQEMFKRVSDQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEE Trimastix_marina --------GQCGNQIGAKFWEVISDEHGIDPTGAYHGESELQLERINVYFNEATGGKYVPRAVLVDLEPGTMDSVRAGPFGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLIAKIREEYPDRMMCTFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTYGDLNHLVSAVMSGITCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLVGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAASDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSVCDIPPKGLKMSVTFIGNSTAIQELFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Trimastix_pyriformis_pyriformis --------GQCGNQIGAKFWEVISDEHGIDPTGNYHGESELQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRAGPFGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLIAKIREEYPDRMMCTFSVVPSPKVSDTVVEPYNATLSVHQLVENADEVMCIDNEALYDICFRTLKLTTPTYGDLNHLVSAVMSGITCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLVGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAASDPRHGRYLTASALFRGRMSSKEVDEQMLNVQNKNSSYFVEWIPNNIKSSICDIPPKGLKMAVTFIGNSTAIQELFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Trimastix_pyriformis_sulcatus --------GQCGNQIGAKFWEVISDEHGIDPTGASHGESDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRAGPFGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQIAHSLGGGTGSGMGTLLIAKIREEYPDRMMCTFSVVPSPKVSDTVVEPYNATLSVHQLVENSDEVMCIDNEALYDICFRTLKLTTPTYGDLNHLVSAVMSGITCCLRFPGQLNSDLRKLAVNLIPFPRLHFFLVGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAASDPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSICDIPPKGLKMAVTFIGNSTAIQELFKRVSEQFTAMFRRKAFLHWYTGEG------------------------------ Trypanosoma_brucei REIVCVQAGQCGNQIGSKFWEVISDEHGVDPTGTYQGDSDLQLERINVYFDEATGGRYVPRSVLIDLEPGTMDSVRAGPYGQIFRPDNFIFGQSGAGNNWAKGHYTEGAELIDSVLDVCCKEAESCDCLQGFQICHSLGGGTGSGMGTLLISKLREQYPDRIMMTFSIIPSPKVSDTVVEPYNTTLSVHQLVENSDESMCIDNEALYDICFRTLKLTTPTFGDLNHLVSAVVSGVTCCLRFPGQLNSDLRKLAVNLVPFPRLHFFMMGFAPLTSRGSQQYRGLSVPELTQQMFDAKNMMQAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFIEWIPNNIKSSVCDIPPKGLKMAVTFIGNNTCIQEMFRRVGEQFTLMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATIEE Volvox_carteri REIVHIQGGQCGNQIGAKFWEVVSDEHGIDPTGTYHGDSDLQLERINVYFNEATGGRYVPRAILMDLEPGTMDSVRSGPYGQIFRPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAESCDCLQGFQVCHSLGGGTGSGMGTLLISKIREEYPDRMMLTFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVLDNEALYDICFRTLKLTTPTFGDLNHLISAVMSGITCCLRFPGQLNADLRKLAVNLIPFPRLHFFMVGFTPLTSRGSQQYRALTVPELTQQMWDAKNMMCAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNVKSSVCDIPPKGLKMSATFIGNSTAIQEMFKRVSEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDASAEE ; END; [ The following blocks are output data for analysis step 1774 ] BEGIN TREES; TITLE Tb6550; LINK TAXA = TaxaForAnalysisStep1774; TREE beta_tubulin = [&R] (Toxoplasma_gondii,(Cyanophora_paradoxa,Stylonychia_lemnae),(((Jakoba_incarcerata,((((Jakoba_libera,Reclinomonas_americana),(Malawimonas_jakobiformis,(Trimastix_marina,(Trimastix_pyriformis_sulcatus,Trimastix_pyriformis_pyriformis)))),(Guillardia_theta,Trypanosoma_brucei)),((Euglena_gracilis,Soginia_sp.),(Plaesiobystra_sp.,(Macropharyngomonas_halophila,Naegleria_gruberi))))),(Volvox_carteri,Pisum_sativum)),(Cercomonas_sp.,(Pythium_ultimum,Chlorarachnion_sp.)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4189] END;