NEXUS
[File created by TreeBASE:  7/26/07  20:58:27]
[Matrix accession#: M809]

BEGIN TAXA;
	TITLE M809;
	DIMENSIONS  NTAX=14;
	TAXLABELS
		Chlamydomonas_reinhardtii_Crein	Chlamydomonas_allensworthii_Cat	Chlamydomonas_allensworthii_21A	Chlamydomonas_allensworthii_Neb	Chlamydomonas_allensworthii_Hon2	Chlamydomonas_allensworthii_Hon9	Chlamydomonas_allensworthii_Chile	Chlamydomonas_allensworthii_Flam	Chlamydomonas_allensworthii_88.10	Chlamydomonas_allensworthii_266	Chlamydomonas_allensworthii_Krueger	Chlamydomonas_allensworthii_LCA	Chlamydomonas_allensworthii_LCH	Chlamydomonas_allensworthii_LCN
	;
END;

BEGIN CHARACTERS;
	TITLE M809;
	DIMENSIONS NCHAR=629;
	FORMAT DATATYPE = DNA MISSING = - GAP = #  ;
	MATRIX
		Chlamydomonas_reinhardtii_Crein           AATCTATCACAATCCACACCGCGAACTAACACTGTTGGCCTCCGTCTGTG-TAAAAGCA-----AACGGGCCAGGTCTGGGCGCAATGTAAAAGTTACGCCTGGCCTGGGT------TGCCGCAA------GGCATCGGTCTCTTATACTAACCAACCAACACCAAACCAAAACTAAATTAAAACCGAGTATCTAGCTTAGAGCTAGTGCTCACTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGGATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAATACGTGAATCATCGAATCTTTGAACGCATATTGCGCTCGAGGCTTCGGCCAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCCCTA-CTCCAACATACACTTGTGTGTTTGGAGCAAGAGCGGACCTGGCTGTCTCGGTGTTTGATTTTCGGATCAGACGCCGGGTCAGCTGAAGTACAGAGGTTGATGCATGGACCCGCTTATGGGCCTCTACTGGGTAGGCAACTCGTTGCTAATGCTTTAGTAGATGGCTTGGAGCTGTGCTTGTCGACCCAAACCAGGAACTTTGGCCCTGTGCCGAAGCAAACCCCTATTTTC
		Chlamydomonas_allensworthii_Cat           AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TAAATT-CGGATCGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC--AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTCTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_21A           AATCTATCAATACCAACACCGAGAACCAATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TTTATT-CTGATCGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC--AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Neb           AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGTTCCG----TTTATT-CGGATCGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTAT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC--AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAGACTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Hon2          AATCTATCAATACCAACACCGAGAACCGATTCGTCTGACC-CCGTC-GTGGCGCAAGCG---ACGACGG-CGCTTGCCGATCCG----TTTATT-CGGATCGGCGATCGGGCTCCGGGGCCTCAAAACCCTAGGGTCGGTCTAT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC--AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGATCTGGCAGTCTCAGTTTGC------------AAAAACTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACT----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Hon9          AATCTATCAATACCAACACCGAGAACCAATTCGTCTGACC-CTGTT-GATGCGCAAGCA---GCAACGG-CGCTTGCCGATGCG----TTAACT-CGGGTCGGTGATCGGGCTCTAGGGCTTAACAACCCTAGGGTCGGTCCCT----GTCCAACAACAACACCAAACCAATACCTCTAACTAAAC-TGCATTCGGCTC--AGCCGGTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGATCTGGCAGTCTCGGTTTGC------------AAAAACCGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACA----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Chile         AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CT-TTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAGCACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT--AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGCCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Flam          AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CT-TTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAGCACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT--AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_88.10         AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAGCACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT--AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCCCAA-------------------TTGGATCGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_266           AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAGCCTTTGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CCAAGCACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT--AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_Krueger       AATCTATCAATAACAACACCGAGAACCATTTCGTCTGACC-CTTTTATAAAC-TTCGGGTTTATAACGG-CGCCTGTTGTTTGG----TTAATT-CTAAGCACCAGGTGGGCTC---GGCTT-------GCCGAGTTGGTCTCT----GTCCAACAACAACACCAAACCAATAATTCTAATTATCC-TGCATTCGGCAT--AGCCGATGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCCCAA-------------------TTGGAACGGATCTGGCAGTCTCAGCTTTTTC--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGGTTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGACCCTCAACAGGAAAACC----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_LCA           AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTCCTAT--GCTTTCGGG--TATAGAAG-CGCTCGGAGCCTAG----TTAATT-CTAAGCTCCGGGTGGGCTC---GGCTTC-----GGCTGGGTTGGTTCCT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA---ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATACCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTG--------ATTAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC-----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_LCH           AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTTCTAT--GCTTTCGGG--TATAGAGG-CGCTCGTTGCCTAG----TTAATT-CTAAGCTCCGGGTGGGCTC---AGCTTC-----GGCTGGGTTGGTTCTT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA---ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATTCCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTT--------AATAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC-----------------ATTAACCTATTTTC
		Chlamydomonas_allensworthii_LCN           AATCTATCAATACCAACACCGAGAACCATTTCGTCTGACC-CTTCTAT--GCTTTCGGG--TATAGAGG-CGCTTGGAGCCTAG----TTAATT-CTAAGCTCCGGGTGGGCTC---GGCTTC-----GGCTGGGTTGGTCCTT----GTCCAACAACAACACCAAACAAATAATTCTAAATAATC-TGCATTCGGCA---ATCGGCTGC-ATCTAACCAAGA-CAACTCTCAACAACGGATATCTTGGCTCTCGCAACGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAAAACCGTGAACCATCGAATCTTTGAACGCATATTGCGCTCGACCCTTCGGGGAAGAGCATGTCTGCCTCAGCGTCGGGTT-AATACTCGCTCCAATACCACA--------------------TTGGAACGGACCTGGCAGTCTCAGTTCTTTG--------ATTAGAGCTGGGTCTGCTGAAGTGCAGAGATTGATGTA-GGACCCGC-TATGGGCCGCAACTGGGTAGGCA-CTCGT-GCTAATTCTT-AGTTGTTGGCTTGGGACT-TGCT-GTCGATCCTCAACAGGAAAAC-----------------ATTAACCTATTTTC
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 629 ; 
 CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;