#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 November 08, 2025; 17:35 GMT TreeBASE (cc) 1994-2008 Study reference: Park M., Culler C., & Pryor B. 2007. A re-examination of the phylogenetic relationship between the causal agents of carrot black rot, Alternaria radicina and A. carotiincultae. Mycologia, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1944] [ The following blocks are input data for analysis step 3991 ] BEGIN TAXA; TITLE TaxaForAnalysisStep3991; DIMENSIONS NTAX=34; TAXLABELS Alternaria_alternate Alternaria_carotiincultae_BMP0064 Alternaria_carotiincultae_BMP0075 Alternaria_carotiincultae_BMP0076 Alternaria_carotiincultae_BMP0078 Alternaria_carotiincultae_BMP0095 Alternaria_carotiincultae_BMP0129 Alternaria_carotiincultae_BMP0130 Alternaria_carotiincultae_BMP0131 Alternaria_carotiincultae_BMP0132 Alternaria_carotiincultae_BMP0133 Alternaria_petroselini Alternaria_radicina_BMP0047 Alternaria_radicina_BMP0055 Alternaria_radicina_BMP0062 Alternaria_radicina_BMP0065 Alternaria_radicina_BMP0066 Alternaria_radicina_BMP0073 Alternaria_radicina_BMP0074 Alternaria_radicina_BMP0079 Alternaria_radicina_BMP0089 Alternaria_radicina_BMP0090 Alternaria_radicina_BMP0093 Alternaria_radicina_BMP0094 Alternaria_radicina_BMP0096 Alternaria_radicina_BMP0097 Alternaria_radicina_BMP0098 Alternaria_radicina_BMP0099 Alternaria_radicina_BMP0104 Alternaria_radicina_BMP0105 Alternaria_radicina_BMP0108 Alternaria_radicina_BMP0111 Alternaria_selini Alternaria_symrnii ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2973] TITLE 'EF-1a'; LINK TAXA = TaxaForAnalysisStep3991; DIMENSIONS NCHAR=243; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . ] Alternaria_alternate TATGGCATCACTTTTCTTTC-ACGCGGCCTGTTGCGCCCACCCGGTGCTTTCTCTGAGCGCGTAGCCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTT--GGGTGGTGGGGATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCCTTCGCGAACTCCAACGCAATGACGCACATGTAATTTCCCCATTCTGGCCACAGCGAGCTAACAAGCCTCACAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0064 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0075 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0076 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0078 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0095 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0129 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0130 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0131 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0132 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_carotiincultae_BMP0133 TATGGCACCACTTTTCTTTC-ACATGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCCCAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_petroselini TATGGCATCACTTTTCTTTC-ACACGGACAGCTACATGCACTCGGTGCTTCCTCTGAGCGCGCAGCCAAAG--TGGCTTATCGCGATGAGGGGCATTTTTTTGGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCCAATTTCTCCATCTTGGCTACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0047 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0055 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0062 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0065 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0066 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0073 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0074 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0079 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0089 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0090 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0093 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0094 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0096 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0097 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0098 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0099 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0104 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0105 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0108 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_radicina_BMP0111 TATGGCACCACTTTTCTTTC-ACACGGACAGTTGCATCCACTCGGTGCTTCCTCTGCGCACGCAGTCAAAGCCTGGCTTATCGCGATGAGGGGCATTTTTT-GGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCTAATTTTCCCATTTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_selini TATGGCATCACTTTTCTTTC-ACACGGACAGCTACATGCACTCGGTGCTTCCTCTGAGCGCGCAGCCAAAG--TGGCTTATCGCGATGAGGGGCATTTTTTTGGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATCCAATTTCTCCATCTTGGCTACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC Alternaria_symrnii TATGGCATCACTTTTTTTTCCACACGGACAGCTATATCCACTCGGTGCTTCCTCTGAGCGCGCAGCCAAAG--TGGCTTATCGCGATGAGGGGCATTTTTTTGGGTGGTGGG-ATGTGCGAACTTTTACGCGCTAGCGCTAGTCCGCATGCGGCGTTCGCGAACTCCAACACCATGACGCACATACAATTTCCCCATCTTGGCCACAGCAAGCTAACAAGCCTCATAGGAAGCCGCCGAACTC ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'EF-1a') = N: 1-243; CODONPOSSET CodonPositions (CHARACTERS = 'EF-1a') = N: 1-243; END; [ The following blocks are output data for analysis step 3991 ] BEGIN TREES; TITLE Tb8763; LINK TAXA = TaxaForAnalysisStep3991; TREE Fig._2 = [&R] (Alternaria_alternate,((Alternaria_symrnii,(Alternaria_selini,Alternaria_petroselini)),((Alternaria_carotiincultae_BMP0133,Alternaria_carotiincultae_BMP0132,Alternaria_carotiincultae_BMP0131,Alternaria_carotiincultae_BMP0130,Alternaria_carotiincultae_BMP0129,Alternaria_carotiincultae_BMP0095,Alternaria_carotiincultae_BMP0078,Alternaria_carotiincultae_BMP0076,Alternaria_carotiincultae_BMP0075,Alternaria_carotiincultae_BMP0064),Alternaria_radicina_BMP0111,Alternaria_radicina_BMP0105,Alternaria_radicina_BMP0104,Alternaria_radicina_BMP0099,Alternaria_radicina_BMP0098,Alternaria_radicina_BMP0108,Alternaria_radicina_BMP0097,Alternaria_radicina_BMP0096,Alternaria_radicina_BMP0094,Alternaria_radicina_BMP0093,Alternaria_radicina_BMP0090,Alternaria_radicina_BMP0089,Alternaria_radicina_BMP0079,Alternaria_radicina_BMP0074,Alternaria_radicina_BMP0073,Alternaria_radicina_BMP0066,Alternaria_radicina_BMP0065,Alternaria_radicina_BMP0062,Alternaria_radicina_BMP0055,Alternaria_radicina_BMP0047))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5002] END;