#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 20, 2025; 2:07 GMT TreeBASE (cc) 1994-2008 Study reference: Santos J.M., Vrandecic K., Cosic J., Duvnjak T., & Phillips A.J. 2011. Resolving the Diaporthe species occurring on soybean in Croatia. Persoonia, 27: 9-19. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10556] [ The following blocks are input data for analysis step 6829 ] BEGIN TAXA; TITLE TaxaForAnalysisStep6829; DIMENSIONS NTAX=42; TAXLABELS Diaporthe_caulivora_Dip1 Diaporthe_caulivora_Dip2 Diaporthe_caulivora_Dpc1 Diaporthe_caulivora_Dpc11 Diaporthe_caulivora_Dpc4 Diaporthe_longicolla_1_2_4_1 Diaporthe_longicolla_1_2_4_2 Diaporthe_longicolla_1_2_4_3 Diaporthe_longicolla_3_27_3_2 Diaporthe_longicolla_PL4 Diaporthe_longicolla_PL7 Diaporthe_longicolla_Pl1a Diaporthe_lusitanicae_GQ250310 Diaporthe_lusitanicae_GQ250311 Diaporthe_melonis_GQ250314 Diaporthe_novem_3_27_3_1 Diaporthe_novem_4_27_3_1 Diaporthe_novem_4_27_3_2 Diaporthe_novem_5_27_3_1 Diaporthe_novem_5_27_3_2 Diaporthe_novem_5_27_3_3 Diaporthe_novem_AS1 Diaporthe_phaseolorum_AF398894 Diaporthe_phaseolorum_AF398895 Diaporthe_phaseolorum_Ar2 Diaporthe_phaseolorum_FAU458 Diaporthe_phaseolorum_PS03 Diaporthe_phaseolorum_PS06 Diaporthe_phaseolorum_PS8 Diaporthe_phaseolorum_PSu1 Diaporthe_phaseolorum_PSu5 Diaporthe_phaseolorum_PSuB9 Diaporthe_phaseolorum_PSuS3 Diaporthe_phaseolorum_PSuS4 Diaporthe_phaseolorum_Su10 Diaporthe_phaseolorum_Su9 Diaporthe_phaseolorum_var_caulivora_AF398889 Leucostoma_niveum_DQ862035 Phomopsis_longicolla_AF398900 Phomopsis_sp_9_DQ286259 Phomopsis_sp_9_GQ250363 Valsa_ambiens_DQ862041 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M7528] TITLE EF1a_Indels; LINK TAXA = TaxaForAnalysisStep6829; DIMENSIONS NCHAR=32; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2 3 4 5" MISSING=? GAP= -; MATRIX [ 10 20 30 ] [ . . . ] Diaporthe_caulivora_Dip1 1011010011101-011000000100010010 Diaporthe_caulivora_Dip2 1011010011101-011000000100010010 Diaporthe_caulivora_Dpc1 1011010011101-011000000100010010 Diaporthe_caulivora_Dpc11 1011010011101-011000000100010010 Diaporthe_caulivora_Dpc4 1011010011101-011000000100010010 Diaporthe_longicolla_1_2_4_1 0110011001101-011101-001001-0111 Diaporthe_longicolla_1_2_4_2 0110011001101-011101-001001-0111 Diaporthe_longicolla_1_2_4_3 0110011001101-011101-001001-0111 Diaporthe_longicolla_3_27_3_2 0110011001101-011101-001001-0111 Diaporthe_longicolla_PL4 0110011001101-011101-001001-0111 Diaporthe_longicolla_PL7 0110011001101-011101-001001-0111 Diaporthe_longicolla_Pl1a 0110011001101-011101-001001-0111 Diaporthe_lusitanicae_GQ250310 00100101-11000111100001-00010110 Diaporthe_lusitanicae_GQ250311 00100101-11000111100001-00010110 Diaporthe_melonis_GQ250314 0110011011101-0111000001111-0111 Diaporthe_novem_3_27_3_1 00100101-11100011110011-00011110 Diaporthe_novem_4_27_3_1 00100101-11000011110011-00011110 Diaporthe_novem_4_27_3_2 00100101-11000011110011-00011110 Diaporthe_novem_5_27_3_1 00100101-11000011110011-00011110 Diaporthe_novem_5_27_3_2 00100101-11000011110011-00011110 Diaporthe_novem_5_27_3_3 00100101-11000011110011-00011110 Diaporthe_novem_AS1 00100101-11000011110011-00011110 Diaporthe_phaseolorum_AF398894 01100111-1101-011101-001001-0111 Diaporthe_phaseolorum_AF398895 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_Ar2 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_FAU458 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PS03 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PS06 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PS8 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PSu1 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PSu5 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PSuB9 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PSuS3 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_PSuS4 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_Su10 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_Su9 0110111011101-0111001001001-0111 Diaporthe_phaseolorum_var_caulivora_AF398889 1011010011101-011000000100010010 Leucostoma_niveum_DQ862035 00000000000001000000100000000000 Phomopsis_longicolla_AF398900 0110011001101-011101-001001-0111 Phomopsis_sp_9_DQ286259 00100101-11000011110011-00011110 Phomopsis_sp_9_GQ250363 00100101-11000011110011-00011110 Valsa_ambiens_DQ862041 00000000000001000000100000000000 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M7527] TITLE EF1a_DNA; LINK TAXA = TaxaForAnalysisStep6829; DIMENSIONS NCHAR=398; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Diaporthe_caulivora_Dip1 ????????????????????AAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTC???????????????????? Diaporthe_caulivora_Dip2 ????????????????????AAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTC???????????????????? Diaporthe_caulivora_Dpc1 ????????????????????AAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTC???????????????????? Diaporthe_caulivora_Dpc11 ????????????????????AAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTC???????????????????? Diaporthe_caulivora_Dpc4 ????????????????????AAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTC???????????????????? Diaporthe_longicolla_1_2_4_1 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_1_2_4_2 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_1_2_4_3 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_3_27_3_2 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_PL4 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_PL7 ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_longicolla_Pl1a ????????????????????AAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTG???????????????????? Diaporthe_lusitanicae_GQ250310 ????????????????????AAGGTCAGTAAACATCACGCATCCCACAGCATGAACTCCACAAAGTCC-TCCATGCGCACATTGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCGTCAC------CCGTCAAG--GCATTTTCACCC-CTCCCTCTGGGTTTTTTTTC-ATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTCCTACACGCAAAACCCTGCTG---GCATTAACCACTCCTTACCACCGCCAA-CACCAACTCTACCACCATGAACCCTATCCAAAGCCCTCCTGGCGAAACGAAC------T-GTCAAGAAAATGACGCTGACTTACTTTTCACCCAGCCGCCGAGCTG???????????????????? Diaporthe_lusitanicae_GQ250311 ????????????????????AAGGTCAGTAAACATCACGCATCCCACAGCATGAACTCCACAAAGTCC-TCCATGCGCACATTGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCGTCAC------CCGTCAAG--GCATTTTCACCC-CTCCCTCTGGGTTTTTTTTC-ATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTCCTACACGCAAAACCCTGCTG---GCATTAACCACTCCTTACCACCGCCAA-CACCAACTCTACCACCATGAACCCTATCCAAAGCCCTCCTGGCGAAACGAAC------T-GTCAAGAAAATGACGCTGACTTACTTTTCACCCAGCCGCCGAGCTG???????????????????? Diaporthe_melonis_GQ250314 ????????????????????AAGGTTAGTAAACATCACCAAACCCGCAGTTTGACCTCCAT--GTCCC-TCCATACGCACATAGAAATCGTTGGCG-CGCG-CTGCCTGCGGGGCTTCGTCACAC----CTGTCCAG--GCATTTTCACCC-CTCCCTCCGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GTGCTTATC-AGACCGCTTATCTCCTCGCACCAAAACCCTGCCGC--ACCT-AGCACACTTC-ACCTGTGACG--CACCAATAGCATCGTTTTTATTCCCAATTGTTGCGCGAAGGAGCTACTCGAA------T-CGCTTGAAAGTCATGCTGACT--CTTTCTGTACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_3_27_3_1 ????????????????????AAGGTCAGTAGATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAC--CCATTTTCACCC-CTCCCTCTGG-TTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTACTAT--GCAAAACCCTGCTT---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCTGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTTTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_4_27_3_1 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTTTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_4_27_3_2 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTTTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_5_27_3_1 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTCTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_5_27_3_2 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTCTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_5_27_3_3 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTCTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_novem_AS1 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTTTCCACACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_AF398894 CATCGAGAAGTTCGAGAAGGAAGGTTAGTAAATACCACCACACCTGCAGCTTGCGCTCCAT--ATCCC-TCTATATGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCAC------CTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGGGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTGGGTAAGGGTTCCTTCAAGTA Diaporthe_phaseolorum_AF398895 CATCGAGAAGTTCGAGAAGGAAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGTGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTGGGTAAGGGTTCCTTCAAGTA Diaporthe_phaseolorum_Ar2 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_FAU458 CATCGAGAAGTTCGAGAAGGAAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGTGGGAGCTTTTCGAC------T-TGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTGGGTAAGGGTTCCTTCAA??? Diaporthe_phaseolorum_PS03 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PS06 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PS8 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PSu1 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PSu5 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PSuB9 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PSuS3 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_PSuS4 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_Su10 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_Su9 ????????????????????AAGGTTAGTAAACATCGCCCAACGGGCACCTTGACCTCCAC--ATCAC-CCCATACGCACA--GAACTCGTTGGCG-CGCG-CTGCCTGCGAGGCTTCGTCACAC----CTGTCAAG--GCATTTTCACCC-CTACCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC-TCACACCAAAACCCTGTCGC--ACCTTACCTCTCTTCCACCAGTGACG--CACCAACAGTATCACCTTCATTCCCATCTGTTGCTCGAGGGAGCTTTTCGAC------T-CGCTTGAAAATGATGCTGACT--CTTTCTGAACAGCCGCCGAGCTG???????????????????? Diaporthe_phaseolorum_var_caulivora_AF398889 CATCGAGAAGTTCGAGAAGGAAGGTTAGTGAATATC--CAAACATCCAGCAAATGCTTCCACTCCCAT-CCCA-GTGCTACTCGCAGCTGTCTGCG-TGCGGCCATTTGCGCCGCATCATCACAC----CTGGAGGC--GCATTTTCACCC-CTCGCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATCTGGGGGGCTTATCTTCCGCCTGCAAAACCCTGTTAC--ATCACCCCTCCCAACCACCATTTCCGC-CACCACTCTTACCACACCTGCCGTCGCCCGCCCACATCAAAGCAAGATGAAAGCCCCAT-TTTTAAAGCATGATGCTGACCTCTTCTCTATATAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTA Leucostoma_niveum_DQ862035 ????????????????????AAGATTGGCGGTATTGGAACAGTGCCCGTCGGCCGTATCGAGACTGGTGTCCTCAAGCCCGGTATGGTCGTTACCTTCGCCCCCGCTGGTGTGACCACTGAGGTCAAGTCCGTCGAGATGCACCACGAGCAGCTCAGTGAGGGTCTC---CCCGGTGACAACGTTGGATTCAACGTCAAGAACGTCTCCGTCAAGGAGATT-CGCCGTGGAAACGTTGCTGGTGACTCCAAGAACGACCCCCCTATGGGAGCCGCTTCTTTCACCGCCCAGGTCATCGTCCTCAACCACCCTGGCCAGGTCGGTGCTGGATACGCACCAGTCCTTGACTGCCACACTGCCCACATTGCTTGCAAGTTCGCCGAGATC??????????? Phomopsis_longicolla_AF398900 CATCGAGAAGTTCGAGAAGGAAGGTCAGTAAATACCACCACACGTGCAGCTTGCGCTCCAT--ATCCC-TCCATGTGCACATAGAAACCGTTGGCG-TGCG-CTGTCTGCGACGCTCCGTCACACCTACCTGTAAAG--GCATTTTCACCC-CTCCCTCTGGATTTT----CCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AGGCCGCTTATCTC---ACACATCAACCCTGTCGC--ACCTTTACCACTGTTCGCCAGTGACA--CACCAATAGCATCACTTTCATTCCCACTTTCTGCTCCAGAGAGCTTTTTGGA------T-CGTTCCAAAATCATGCTGACT--CTTTCTACACAGCCGCCGAGCTGGGTAAGGGTTCCTTCAAGTA Phomopsis_sp_9_DQ286259 ???????????????????????GTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTCTCCACACAGCCGCCGAGCTGGGTAAGGGTTC????????? Phomopsis_sp_9_GQ250363 ????????????????????AAGGTCAGTAAATATCGCACATCCCACAGCATGAACTCCACCAAGCCC-ACCGTGCGCACATCGTCATCATTGGTG-CGCGACTGCCTGCGCGGCTTCATCAC------CCCTCAAA--CCATTTTCACCC-CTCCCTCTGGGTTTTTTTTCCATTTTCAGTG-CGGGTGCGGGGT-GCGCTTATC-AG-CCGCTTATCTCCTAT--GCAAAACCCTGCTG---GCATTAACCACTCCTTGCCACCGCCAA-CACCAACTCTACCACTTTCAACCCTATC---AATCTCCCAGGCGAAACGAAC------T-GTCAAGAATATGAAGCTGACTTACTCTCCACACAGCCGCCGAGCTG???????????????????? Valsa_ambiens_DQ862041 ????????????????????AAGATTGGCGGTATTGGCACAGTGCCCGTCGGCCGTATCGAGACTGGTATCCTCAAGCCCGGTATGGTCGTCACCTTCGCTCCCGCCAACGTCACCACTGAGGTGAAGTCCGTCGAGATGCACCACGAGCAGCTCACCGAGGGTCTC---CCCGGTGACAACGTCGGCTTCAACGTCAAGAACGTCTCCGTCAAGGAGATT-CGTCGTGGCAACGTTGCCGGTGACACCAAGAACGACCCCCCTCTGGGTTGTGCTTCCTTCACCGCCCAGGTCATCGTCCTGAACCACCCCGGTCAGGTCGGTGCTGGATACGCACCAGTCCTCGATTGCCACACTGCCCACATTGCTTGCAAGTTCGCCGAGATC??????????? ; END; [ The following blocks are output data for analysis step 6829 ] BEGIN TREES; TITLE EF1a; LINK TAXA = TaxaForAnalysisStep6829; TREE Fig._1 = [&R] (Leucostoma_niveum_DQ862035:0.021757,Valsa_ambiens_DQ862041:0.065482,((Diaporthe_caulivora_Dip1:0.002543,Diaporthe_caulivora_Dpc11:0.002515,Diaporthe_caulivora_Dip2:0.002566,Diaporthe_caulivora_Dpc4:0.002459,Diaporthe_caulivora_Dpc1:0.002562,Diaporthe_phaseolorum_var_caulivora_AF398889:0.002417)1.00:0.27033,(((Diaporthe_phaseolorum_AF398894:0.010534,(Diaporthe_longicolla_1_2_4_1:0.002669,Diaporthe_longicolla_1_2_4_2:0.002578,Diaporthe_longicolla_1_2_4_3:0.002582,Diaporthe_longicolla_PL7:0.002585,Diaporthe_longicolla_3_27_3_2:0.002688,Diaporthe_longicolla_PL4:0.002592,Diaporthe_longicolla_Pl1a:0.002538,Phomopsis_longicolla_AF398900:0.00263)0.91:0.013594)1.00:0.11479,(Diaporthe_melonis_GQ250314:0.083627,((Diaporthe_phaseolorum_FAU458:0.005392,Diaporthe_phaseolorum_AF398895:0.002729)0.94:0.006528,(Diaporthe_phaseolorum_PSu5:0.002678,Diaporthe_phaseolorum_Ar2:0.002766,Diaporthe_phaseolorum_PSuS4:0.002627,Diaporthe_phaseolorum_PSuS3:0.002659,Diaporthe_phaseolorum_PSuB9:0.002692,Diaporthe_phaseolorum_Su10:0.002571,Diaporthe_phaseolorum_Su9:0.002683,Diaporthe_phaseolorum_PSu1:0.00273,Diaporthe_phaseolorum_PS8:0.002631,Diaporthe_phaseolorum_PS03:0.002648,Diaporthe_phaseolorum_PS06:0.002675)0.62:0.005773)1.00:0.052259)0.52:0.031826)1.00:0.15359,((Diaporthe_novem_AS1:0.002643,Diaporthe_novem_4_27_3_2:0.002603,Diaporthe_novem_4_27_3_1:0.002607,Diaporthe_novem_3_27_3_1:0.01873,(Diaporthe_novem_5_27_3_1:0.002632,Diaporthe_novem_5_27_3_2:0.002569,Diaporthe_novem_5_27_3_3:0.002607,Phomopsis_sp_9_GQ250363:0.002573,Phomopsis_sp_9_DQ286259:0.002608)0.93:0.005308)1.00:0.058625,(Diaporthe_lusitanicae_GQ250311:0.002562,Diaporthe_lusitanicae_GQ250310:0.002664)1.00:0.036399)1.00:0.143477)0.91:0.173151)1.00:1.240306); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr26547] END;