#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 July 01, 2025; 7:56 GMT TreeBASE (cc) 1994-2008 Study reference: Brumfield R., & Edwards S. 2007. Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution, 61(2): 346-367. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1759] [ The following blocks are input data for analysis step 3506 ] BEGIN TAXA; TITLE TaxaForAnalysisStep3506; DIMENSIONS NTAX=33; TAXLABELS Cymbilaimus_lineatus Frederickena_unduligera Sakesphorus_bernardi Sakesphorus_canadensis Sakesphorus_cristatus Sakesphorus_luctuosus Sakesphorus_melanonotus Sakesphorus_melanothorax Thamnomanes_caesius Thamnoophilus_doliatus Thamnophilus_aethiops Thamnophilus_amazonicus Thamnophilus_aroyae Thamnophilus_atrinucha Thamnophilus_bridgesi Thamnophilus_caerulescens Thamnophilus_cryptoleucus Thamnophilus_divisorius Thamnophilus_insignis Thamnophilus_multistriatus Thamnophilus_murinus Thamnophilus_nigriceps Thamnophilus_nigrocinereus Thamnophilus_palliatus Thamnophilus_praecox Thamnophilus_punctatus Thamnophilus_ruficapillus Thamnophilus_schistaceus Thamnophilus_stictocephalus Thamnophilus_tenuepunctatus Thamnophilus_torquatus Thamnophilus_unicolor Thamnophilus_zarumae ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1663] TITLE nd3a; LINK TAXA = TaxaForAnalysisStep3506; DIMENSIONS NCHAR=367; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Cymbilaimus_lineatus TACTCATCCTAGCCTCATCCCTAAGTATCATCCTAACCCTACTAAACTTTTGACTAGCCCAAACAAACCCAAATTCAGAAAAACTCTCACCATATGAATGTGGCTTCGACCCTTTAGGTTCAGCTCGACTCCCATTCTCCATCCGATTCTTCCTAGTCGCTATTCTATTCCTCCTCTTCGACCTAAAAATCGCTCTCTTATTACCTCTCCCCTGAGCCACTCAACTCCAATCACCCCTCACTACCCTAACATGATCATCCATTATCATTCTCCTCCTTACACTAGGTCTAGTATACGAATGAACTCAAGGAGGCCTAGAATGAGCAGAATAACAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Frederickena_unduligera TACTCACCTTATCCGCATCACTAAGCATCATCCTAACTCTACTAAATTTCTGACTAGCCCAAACAAACCCCAACTCAGAAAAACTGTCACCATATGAATGTGGATTTGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATTCGTTTCTTTCTAATCGCTATCCTATTCCTCCTCTTCGATCTAGAAATCGCTCTCCTATTACCCCTCCCCTGAGCTACCCAACTCCAATCTCCCCTCACTACCCTAACATGATCATCTACTATTATTCTTCTTCTTACACTAGGCCTAGTATATGAATGAACTCAAGGAGGACTAGAATGAGCAGAATAACAATAGAAAGTTAGTCTAACAAAGACAGTTGATTT Sakesphorus_bernardi TACTTGCCCTATCCTCATCACTAAGCATTATCCTAAGTCTTCTAAACTTCTGACTGGCTCAAACAAAACCCGATTTAGAAAAACTTTCACCATACGAATGTGGCTTCGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTCGCCATCTTGTTCCTCCTATTTGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCCACCCAACTTCAATCCCCCCTCACCACCCTAACATGATCCTCTATCATTATCCTCCTTCTCACACTAGGCCTAGTATATGAGTGAATTCAAGGAGGCTTAGAATGAGCAGAGTAACGACAGAAAGTTAGTCTAACAAAGACGGTTGATTT Sakesphorus_canadensis TACTCACACTATCTTCATCACTAAGTATCATCCTAACCCTCTTAAACTTCTGACTAGCTCAAACAAACCCTGACTCAGAAAAACTCTCCCCCTACGAATGTGGCTTCGACCCCCTAGGATCTGCTCGACTCCCATTCTCCATCCGCTTCTTCCTAGTTGCTATCCTATTCCTCCTATTCGACCTAGAAATTGCCCTCCTGTTACCCCTCCCATGAGCTACCCAACTTCAATTTCCCCTCACTACCCTAACATGATCATCTACCATTATTCTCCTTCTTACATTAGGCCTAGTATATGAATGAACTCAAGGAGGCTTAGAATGAGCAGAATAACAGCAGAAAGTTAGTCTAATAAAGACAGTTGATTT Sakesphorus_cristatus TACTTGCCCTATCTTCATCTCTAAGCATTATTCTAACCCTCCTAAATTTCTGACTAGCCCAAACAAACCCTAACTCAGAAAAGCTCTCACCATACGAATGCGGCTTCGACCCATTAGGCTCTGCCCGACTTCCATTCTCCATCCGCTTCTTCCTAGTCGCTATTTTGTTTCTCCTATTTGACCTAGAAATCGCCCTTTTACTGCCCCTCCCCTGAGCTACCCAACTTCAATCCCCCCTTACTACCTTGACATGATCATCCATTATTATTCTCCTTCTCACACTAGGCCTAGTATACGAATGAATTCAAGGAGGCTTAGAATGAGCAGAATAAC?????????????????????????????????? Sakesphorus_luctuosus CACTTACATTATCTTCATCATTAAGCATCATCCTAATCTTCTTAAACTTCTGACTAGCCCAAACAAACCCTGACTCAGAAAAACTCTCCCCCTACGAATGTGGCTTCGACCCCCTAGGATCTGCTCGACTCCCATTCTCCATCCGCTTCTTCCTAATCGCCATCCTATTCCTCCTGTTCGACCTAGAAATCGCCCTCTTATTACCCCTCCCATGAGCCACCCAACTTCAATTTCCCCTCACTACTTTAACATGATCCTCTACCATTATTCTCCTTCTCACATTAGGCCTAGTATATGAATGAACTCAAGGAGGCTTAGAATGAGCAGAATAACAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Sakesphorus_melanonotus TACTTACCCTATCTTCATCATTAAGCATTATCCTAACCTTCCTAAACTTCTGACTAGCTCAGACAAGCCCCGATTCAGAAAAACTCTCCCCCTACGAATGTGGCTTCGACCCACTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTAGCCATCTTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCCACTCAACTTCAATCCCCCCTCACTACCCTGTCATGATCATCTACCATTATTCTCCTCCTCACACTAGGCTTAATTTATGAATGAATTCAAGGGGGCTTAGAATGAGCAGAATAATAACAGAAAGTTAGTCTAATAAAGACAGTTGATTT Sakesphorus_melanothorax TACTCACTCTATCTTCATCACTAAGTATTATCCTAACCCTCCTAAATTTCTGACTAGCCCAGACAAACCCTAATTCAGAAAAACTCTCACCCTACGAATGTGGCTTCGA??????????????????????CCATTCTCCATCCGCTTTTTCCTAGTCGCCATCTTGTTCCTCCTATTTGACCTAGAAATCGCCCTCCTACTGCCCCTCCCCTGAGCTACTCAACTT{CG}AAT{CT}{CT}CCCCTCACTACCCTGACATGATCATCTATCATCATTCTCCTTCTGACACTAGGCTTAGTGTATGAATGAGCTCAAGGGGGCTTAGAGTGAGCAGAATAACAGCAGAAAGT???????????????????????? Thamnomanes_caesius TACTCACACTATCTTCATCACTAAGCATTATTCTAACCCTACTAAATTTCTGACTGGCCCAAACAAATCCAGACTCAGAAAAACTTTCACCATACGAATGTGGCTTCGATCCACTAGGCTCTGCTCGACTCCCATTCTCCATCCGCTTCTTCCTAGTCGCTATCCTATTCCTTCTCTTCGACCTAGAAATCGCCCTCTTATTACCTCTCCCCTGAGCTACCCAACTACAATCACCTCTCACCACCCTAACATGATCATCTGCCATCATCCTCCTCCTCACACTAGGCCTAGTCTATGAATGAACTCAAGGAGGCCTAGAATGAGCAGAATAGCAGCAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnoophilus_doliatus TACTTACCCTATCTTCATCACTAAGCATTATCCTAATCTTCCTAAACTTCTGACTAGCTCAAACAAACCCCAACCCAGAAAAACTTTCACCATACGAATGTGGCTTCGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTCGCTATCTTATTCCTCCTATTCGACCTAGAAATCGCCCTCCTACTGCCACTCCCCTGAGCCACTCAACTTCAATCCCCCCTTATCACCCTAACATCATCATCTATTATTATCCTCCTCCTCACGCTAGGCCTAGTATATGAATGAATGCAAGGAGGCTTAGAGTGAGCAGAGTAATAGCAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_aethiops TACTTACCCTATCTTCATCACTAAGCATTATTTTAACCCTCCTAAATTTCTGACTAGCTCAAACAAACCCTAACTCAGAAAAACTCTCACCATATGAATGTGGATTCGACCCGCTAGGCTCTGCCCGACTTCCATTCTCTATCCGCTTTTTCCTAGTCGCCATCCTGTTCCTTCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTTACCACCCTGACATGGTCATCCATCATCATTCTCCTTCTCACACTAGGCCTAGTATATGAATGAATTCAAGGAGGCCTAGAATGAGCAGAGTAACAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_amazonicus TACTTACTCTATCTTCATCACTAAGCATTATCCTAACCCTCCTAAATTTCTGACTAGCTCAGACAAACCCTAGTTCAGAAAAGCTCTCACCATACGAATGTGGTTTCGACCCACTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTCGCCATCTTGTTCCTCTTATTCGACCTAGAGATCGCCCTTCTACTACCACTCCCCTGAGCCACTCAACTTCAATCCCCCCTCACTACCCTAACATGATCATCTACCATCATTCTCCTCCTCACACTAGGCCTAGTATATGAATGAATTCAAGGAGGCTTAGAATGAGCAGAGTAATACCAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_aroyae TACTTATTTTATCTTCATCACTAAGCATCATCCTAACCCTCCTAAATTTTTGGCTAGCTCAAACGAACCCTAACTCAGAAAAACTCTCACCATATGAATGTGGATTTGACCCACTAGGCTCTGCCCGACTTCCATTCTCTATCCGCTTTTTCCTAGTCGCCATCCTGTTCCTCCTATTCGACCTGGAAATCGCCCTTTTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTTACTACCCTGACATGGTCATCTGTCATCATTCTTCTCCTCACACTAGGCCTAGTATATGAGTGAATTCAAGGGGGCTTAGAATGAGCCGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_atrinucha TACTTACCCTATCTTCATCACTAAGCATTATCCTAACCCTCCTAAACTTCTGACTAGCCCAGACAAACCCCAACTCAGAGAAACTTTCCCCATACGAATGTGGCTTCGACCCCCTAGGCTCCGCCCGACTCCCATTCTCTATTCGCTTTTTCCTAGTCGCTATCTTATTCCTCCTATTTGACCTAGAAATTGCCCTTCTACTACCTCTCCCCTGAGCCACTCAACTCCAATTCCCCCTCACTACCCTAACATGATCATCTATTATTATCCTCCTCCTCACACTAGGCCTAGTATATGAATGAATCCAAGGAGGATTAGAATGAGCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_bridgesi TACTTACCTTATCCTCATCACTAAGCATCATCCTAACCCTCCTAAACTTCTGACTCGCTCAAACAAACCCAGACTCAGAAAAACTTTCACCGTACGAATGCGGCTTCGACCCTCTAGGCTCTGCCCGACTCCCATTTTCCATCCGCTTTTTCCTAGTCGCCATCCTATTCCTCCTATTCGACCTAGAGATTGCCCTTCTACTGCCACTCCCCTGAGCCACCCAACTCCAATCCCCTCTCACTACCCTAACATGATCATCTATCATTATCCTCCTCCTCACACTAGGCCTAGTATATGAATGGATTCAAGGAGGATTAGAATGATCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_caerulescens TACTCATTCTATCTTCATCACTAAGCATTATCCTAACCCTCCTAAACTTCTGACTAGCTCAAACAAACCCTAATTCAGAAAAACTCTCACCATATGAATGTGGATTCGATCCACTAGGCTCTGCCCGACTTCCATTCTCCATCCGCTTTTTCCTAGTCGCCATCCTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTCACTACCCTAACATGATCCTCTATCATCATTCTTCTCCTCACACTAGGTCTAGTATATGAATGAACTCAAGGGGGCTTAGAATGAGCAGAGTAGTAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_cryptoleucus TACTCACCCTATCTTCATCACTAAGTATCATCCTAACCCTCCTAAACTTCTGACTAGCTCAGACAAACCCCAACTCAGAAAAACTTTCACCATATGAGTGTGGCTTTGACCCATTAGGCTCTGCCCGACTTCCATTCTCTATCCGCTTTTTCTTAGTCGCCATCTTATTCCTCCTATTCGACCTAGAAATCGCTCTTTTACTACCACTCCCCTGAGCTACCCAACTTCAATCCCCCCTCACTACCCTAACATGATCGTCTATCATCATTCTCCTCCTCACACTAGGCCTAGTATATGAATGAGTTCAAGGGGGTTTAGAATGAGCAGAATAGTAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_divisorius TACTCGCCCTATCCTCATCACTAAGCATTATCCTAACCCTCCTAAACTTCTGACTAGCTCAGACAAACCCTAATTTAGAAAAACTCTCACCATACGAATGTGGCTTCGACCCACTAGGCTCTGCCCGACTTCCCTTTTCCATCCGCTTCTTCTTAGTCGCCATCCTGTTCCTCCTATTCGATCTAGAAATCGCCCTTCTACTACCACTTCCCTGAGCTACTCAACTTCAATCCCCCCTAACTACCCTGACATGATCATCTGCCATCATTCTCCTCCTCACATTAGGCTTAGTATATGAATGAATCCAAGGGGGCTTAGAATGAGCAGAATAG??????????????????????????????????? Thamnophilus_insignis TACTTACCCTATCTTCATCACTAAGCATTATCCTAACCCTCCTAAATTTCTGGCTAGCCCAGACAAACCCTGACTCAGAAAAACTCTCACCATACGAATGTGGCTTCGACCCACTAGGCTCTGCCCGACTCCCGTTCTCCATCCGCTTTTTCCTAGTCGCCATCTTGTTCCTACTATTCGATTTAGAAATCGCCCTTCTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTCACTACCCTAACATGATCATGTATCATCATTCTCCTCCTCACACTAGGCTTAGTATATGAATGAATTCAAGGGGGCTTAGAATGAGCAGAGTAATGACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_multistriatus TACTTACCCTATCTTCATCACTAAGCATTATCCTAATCTTCCTAAACTTCTGACTGGCTCAAATAAACCCAAACCCAGAGAAACTCTC{AC}CCCTACGAATGTGGCTTCGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAATCGCTATCCTATTTCTCCTATTCGACCTAGAAATCGCCCTCTTGCTACCACTCCCCTGAGCAACTCAACTTGAATTTCCCCTCATTACCCTAACATGGTCCTCTATCATTATTCTCCTCCTCACACTAGGCCTAGTGTATGAATGAATGCAAGGAGGACTAGAATGAGCAGAGTAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_murinus TACTCACCCTATCTGCATCATTAAGCATTATCCTAACCTTTCTAAATTTCTGACTAGCCCAAACAAATCCCAACTCAGAAAAACTTTCACCATACGAATGCGGCTTCGACCCACTAGGATCTGCCCGACTCCCATTCTCCATCCGCTTTTTCTTAGTTGCTATTTTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCGACTCAACTTCAATTCCCCCTCACTACCCTAACATGATCATCCATTATTATTCTCCTCCTCACTCTAGGCCTAGTCTATGAATGAATTCAAGGGGGCTTAGAATGAGCAGAGTAATGACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_nigriceps TACTCACCCTATCTTCATCACTAAGCATTATCCTAACCCTCCTAAATTTCTGACTAGCCCAAACAAACCCTAACCCAGAAAAACTTTCACCATACGAATGTGGCTTCGATCCACTAGGTTCCGCCCGACTCCCATTCTCCATCCGCTTTTTTCTAGTCGCCATCTTATTCCTCCTATTTGACCTAGAAATCGCCCTTCTACTGCCTCTCCCCTGAGCTACTCAACTTCAATCTCCCCTCACTACCTTGACATGATCATCTATCATCATCCTTCTCCTCACACTAGGCCTAGTATATGAATGAATTCAAGGGGGCTTAGAATGAGCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_nigrocinereus TACTCACCCTATCTTCATCACTAAGTATCATCCTAACCCTCCTAAACTTCTGACTAGCTCAGACAAACCCCAACTCAGAAAAACTTTCACCATATGAGTGTGGCTTTGACCCATTAGGCTCTGCCCGACTTCCATTCTCTATCCGCTTTTTCTTAGTCGCCATCTTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTCACTACCCTAACATGATCGTCTATCATCATTCTCCTCCTCACACTAGGCTTAGTATATGAGTGAATTCAAGGGGGCTTAGAATGAGCAGAATAGTAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_palliatus TACTTACCCTATCTTCATCACTAAGCATTATCCTAATCTCCCTAAACTTCTGACTAGCTCAAACAAACCCAAACTCAGAGAAACTTTCACCATACGAATGTGGCTTCGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTTGCTATCCTATTCCTCCTATTCGACCTAGAAATCGCCCTCTTGCTACCACTCCCCTGAGCAACTCAACTTCAATTCCCTCTCATCACCCTGACATGATCCTCTATCATTATTCTCCTCCTCACACTAGGCCTAGTGTACGAATGAATGCAAGGAGGACTAGAATGAGCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_praecox TACTCACCCTATCTTCATCACTAAGCATTATCCTAACCCTCTTAAATTTCTGACTAGCCCAGACAAACCCTAATTCAGAAAAACTCTCACCATACGAATGTGGCTTTGATCCACTAGGTTCCGCTCGACTCCCATTCTCCATCCGCTTTTTTCTAGTCGCCATCTTATTCCTCCTATTTGACCTAGAAATCGCCCTTCTACTGCCACTCCCCTGAGCTACTCAACTTCAAACTCCTCTCACTACCCTGACATGATCATCCATCATCATTCTTCTCCTCACACTAGGCTTAGTATATGAATGGATCCAAGGGGGCTTAGAATGGGCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_punctatus TACTTACCCTATCTTCATCACTAAGTCTTATCCTAACCCTCCTAAATTTCTGGCTAGCCCAAACAAGCCCTGACTCAGAAAAACTTTCACCATACGAATGTGGCTTCGACCCACTAGGCTCTGCCCGACTTCCATTCTCCATCCGCTTCTTCCTAGTCGCCATCCTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCATGAGCTACTCAGCTTCAATCCCCCCTCACCACCTTGACATGATCATTTGCCATCATTCTCCTTCTCACACTAGGCCTGGTATATGAATGAATTCAAGGGGGTTTAGAATGAGCAGAGTAACAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_ruficapillus TACTTACCTTATCTTCATCACTAAGCATTATCCTAATCTTCCTAAACTTCTGACTAGCTCAAACAAACCCAAACTCAGAAAAACTTTCACCATACGAATGTGGCTTCGATCCCCTAGGCTCTGCCCGACTTCCATTCTCCATCCGCTTTTTCTTAGTCGCTATCTTATTCCTCCTATTTGACCTGGAAATCGCCCTTTTACTACCACTCCCCTGAGCCACTCAACTTCAATCCCCCCTCGTTACCCTAACATGATCATCCATTATTATTCTCCTCCTCACACTAGGCCTAGTATATGAATGAATGCAAGGAGGCTTAGAATGAGCAGAGTAACAACAGAAAGTTAGTCTAACTAAGACAGTTGATTT Thamnophilus_schistaceus TACTTACTTTATCTGCATCACTAAGCATCATCCTAACCCTTCTAAATTTCTGACTAGCCCAGACAAATCCCAACTCAGAGAAACTTTCACCATACGAATGTGGCTTTGACCCGCTAGGTTCTGCCCGTCTCCCATTCTCCATCCGCTTTTTTTTAGTCGCTATCTTATTCCTCCTATTCGACTTAGAAATCGCCCTTTTATTACCACTCCCTTGAGCTACCCAACTCCAATTCCCCCTCACTACCCTGACATGAACATCTATCATTATTCTCCTCCTTACACTAGGCCTAATCTATGAGTGAATTCAAGGGGGCTTGGAATGAGCAGAATAATGACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_stictocephalus TACTTACCCTATCCTCATCACTAAGTGTTATCCTAACCCTCCTAAACTTCTGACTAGCCCAAACAAGCCCTGACTCAGAAAAACTTTCACCATACGAATGTGGCTTCGACCCACTAGGCTCTGCCCGGCTTCCATTCTCCATCCGCTTCTTCCTAGTCGCCATTCTATTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTTCCACTCCCATGAGCTACTCAACTTCAATCCCCCCTCACCACCTTGACATGATCATCTACCATCATTCTCCTTCTCACACTAGGCCTAGTATATGAATGAATTCAAGGGGGTCTAGAATGAGCAGAGTAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_tenuepunctatus TACTTACCCTATCTTCATCACTAAGCATTATCCTAATCTCCCTAAACTTCTGACTAGCTCAAACAAACCCAAACTCAGAGAAACTTTCACCATACGAATGTGGCTTTGACCCCCTAGGCTCTGCCCGACTCCCATTCTCCATCCGCTTTTTCCTAGTTGCTATCCTATTCCTCCTATTCGACCTAGAAATCGCCCTCTTGCTACCACTCCCCTGAGCAACTCAACTTCAATTCCCTCTCATTACCCTGACATGATCCTCTATCATTATTCTCCTCCTCACACTAGGCCTAGTGTACGAATGAATGCAGGGAGGACTAGAATGAGCAGAATAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_torquatus TACTTACCTTATCTTCATTACTAAGCATTATCCTAATTTTCCTGAACTTCTGACTAGCTCAAACAAACCCAAACTCAGAAAAACTTTCACCATACGAATGTGGCTTCGATCCCCTAGGCTCTGCCCGACTTCCATTCTCCATCCGCTTTTTCCTAGTCGCTATCTTATTCCTACTATTTGACCTAGAAATCGCCCTCTTACTACCACTCCCCTGAGCCACTCAACTTCAATCCCCCCTCGTTACCCTAACATGATCATCCATTATTATTCTCCTCCTCACACTAGGCCTAGTATATGAATGAATGCAAGGGGGCTTAGAATGAGCAGAGTAACAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_unicolor TACTTACCATATCTTCATCACTAAGTATCATCCTAACCCTCCTAAACTTCTGACTAGCTCAAACGAACCCTAACTCAGAAAAACTCTCACCATATGAATGCGGATTCGACCCACTAGGCTCCGCCCGACTTCCATTCTCTATCCGCTTTTTCCTAGTCGCTATCCTGTTCCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCCTGAGCTACTCAACTTCAATCCCCCCTCACCACTCTAACATGATCATCTGCCATCATCCTCCTCCTCACACTAGGCCTAGTATATGAATGAATTCAAGGGGGCTTAGAATGAGCAGAGTAATGACAGAGAGTTAGTCTAACAAAGACAGTTGATTT Thamnophilus_zarumae TACTTACCCTATCTTCATCACTAAGTATCATCCTAATCTTCCTAAACTTCTGGCTAGCCCAAACAAACCCCAACTCAGAGAAACTTTCACCATACGAATGTGGCTTCGACCCCCTAGGCTCTGCTCGACTCCCATTCTCCATTCGTTTTTTCCTAATCGCTATCCTATTTCTCCTATTCGACCTAGAAATCGCCCTTTTACTACCACTCCCATGAGCCACTCAACTTCAATTCCCCCTCATTACCCTAACATGATCCTCTATTATCATTCTCCTCCTCACACTAGGCCTAGTATATGAATGAATGCAAGGAGGACTAGAATGAGCAGAGTAATAACAGAAAGTTAGTCTAACAAAGACAGTTGATTT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = nd3a) = N: 1-367; CODONPOSSET CodonPositions (CHARACTERS = nd3a) = N: 1-367; END; [ The following blocks are output data for analysis step 3506 ] BEGIN TREES; TITLE Tb8279; LINK TAXA = TaxaForAnalysisStep3506; TREE Fig._2a_2 = [&R] (Cymbilaimus_lineatus,((Frederickena_unduligera,((((Sakesphorus_bernardi,(Thamnoophilus_doliatus,(((Thamnophilus_palliatus,Thamnophilus_tenuepunctatus),Thamnophilus_multistriatus),Thamnophilus_zarumae),(Thamnophilus_ruficapillus,Thamnophilus_torquatus))),((((((((Thamnophilus_aethiops,(Thamnophilus_aroyae,Thamnophilus_unicolor)),Thamnophilus_caerulescens),(Thamnophilus_punctatus,Thamnophilus_stictocephalus)),Thamnophilus_divisorius),(((Thamnophilus_nigriceps,Thamnophilus_praecox),Sakesphorus_melanothorax),Sakesphorus_cristatus)),Thamnophilus_amazonicus,Thamnophilus_insignis),(Thamnophilus_cryptoleucus,Thamnophilus_nigrocinereus)),((Thamnophilus_murinus,Thamnophilus_schistaceus),Sakesphorus_melanonotus))),(Thamnophilus_atrinucha,Thamnophilus_bridgesi)),(Sakesphorus_canadensis,Sakesphorus_luctuosus))),Thamnomanes_caesius)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4661] END; BEGIN TREES; TITLE Tb8279; LINK TAXA = TaxaForAnalysisStep3506; TREE Fig._2a_3 = [&R] (Cymbilaimus_lineatus,((Frederickena_unduligera,((((Sakesphorus_bernardi,((((((((Thamnophilus_aethiops,(Thamnophilus_aroyae,Thamnophilus_unicolor)),Thamnophilus_caerulescens),(Thamnophilus_punctatus,Thamnophilus_stictocephalus)),Thamnophilus_divisorius),(((Thamnophilus_nigriceps,Thamnophilus_praecox),Sakesphorus_melanothorax),Sakesphorus_cristatus)),Thamnophilus_amazonicus,Thamnophilus_insignis),(Thamnophilus_cryptoleucus,Thamnophilus_nigrocinereus)),((Thamnophilus_murinus,Thamnophilus_schistaceus),Sakesphorus_melanonotus))),(Thamnoophilus_doliatus,(((Thamnophilus_palliatus,Thamnophilus_tenuepunctatus),Thamnophilus_multistriatus),Thamnophilus_zarumae),(Thamnophilus_ruficapillus,Thamnophilus_torquatus))),(Thamnophilus_atrinucha,Thamnophilus_bridgesi)),(Sakesphorus_canadensis,Sakesphorus_luctuosus))),Thamnomanes_caesius)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4660] END; BEGIN TREES; TITLE Tb8279; LINK TAXA = TaxaForAnalysisStep3506; TREE Fig._2a_1 = [&R] (Cymbilaimus_lineatus,((Frederickena_unduligera,(((Sakesphorus_bernardi,((((((((Thamnophilus_aethiops,(Thamnophilus_aroyae,Thamnophilus_unicolor)),Thamnophilus_caerulescens),(Thamnophilus_punctatus,Thamnophilus_stictocephalus)),Thamnophilus_divisorius),(((Thamnophilus_nigriceps,Thamnophilus_praecox),Sakesphorus_melanothorax),Sakesphorus_cristatus)),Thamnophilus_amazonicus,Thamnophilus_insignis),(Thamnophilus_cryptoleucus,Thamnophilus_nigrocinereus)),((Thamnophilus_murinus,Thamnophilus_schistaceus),Sakesphorus_melanonotus)),(Thamnoophilus_doliatus,(((Thamnophilus_palliatus,Thamnophilus_tenuepunctatus),Thamnophilus_multistriatus),Thamnophilus_zarumae),(Thamnophilus_ruficapillus,Thamnophilus_torquatus))),(Thamnophilus_atrinucha,Thamnophilus_bridgesi)),(Sakesphorus_canadensis,Sakesphorus_luctuosus))),Thamnomanes_caesius)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4662] END;