NEXUS
[File created by TreeBASE:  7/26/07  20:58:22]
[Matrix accession#: M792]

BEGIN TAXA;
	TITLE M792;
	DIMENSIONS  NTAX=13;
	TAXLABELS
		Ramalinora_glaucolivida	Lecanora_garovaglii	Ramalina_sinensis	Ramalina_montagnei	Ramalina_menziesii	Ramalina_intermedia	Ramalina_leptocarpha	Lecanora_varia	Lecanora_polytropa	Lecanora_contractula	Lecanora_muralis	Ramalina_fraxinea	Lecanora_glabrata
	;
END;

BEGIN CHARACTERS;
	TITLE M792;
	DIMENSIONS NCHAR=365;
	FORMAT DATATYPE = DNA MISSING = ? GAP = -  ;
	MATRIX
		Ramalinora_glaucolivida       AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACCC-TCAAGCGTAA-GCTTGGTATTGGG-T-CTTCGCCGTCCC--CCTCGGGGGGTGGCGG-GCCCGAAAGACAGTGGCGGTCCCCGG-G-GATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGAA-C-CGTT--TGGA-G-CC-GGCCAGACAAC---------AAAAA-TT--T-CTA--TGATT----
		Lecanora_garovaglii           AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCC-TCAAGC-TCA-GCTTGGTATTGGG-A-CTTCGC---CT-----T---CC-GAGGCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCG-T--C-GT-GACC-GGCCAGA--ACG-----CCCA-AAACTTT-TTCAA--TGATTGACC
		Ramalina_sinensis             AAAA-CTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCACTCAAGCGT-A-GCTTGGTATTGGGTT-CTTCGC---CCGGGG-T-CTCCCGCGGCGT-GCCCGAAAAGCATTGGCGGTCC--GGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGCCTCGCC-C--C-G-GGTCC-GGCCAGACAACC-----CCCACATATAT-CT-CAC---GATTGACC
		Ramalina_montagnei            AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-A-GCTTGGTATTGGGTT-TTTCGC---CGGGGGCTTTTCCC-CAGCGT-GCCCGAAAAGCATTGGCGGTCC--GGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGCCTCGTG-C--T-GTGG-CC-GGCCAGACAACC-----CCCCCAT--AT-CT-CAC---GATTGACC
		Ramalina_menziesii            AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-A-GCTTGGCATTGGGTC-ATTCGC---CCGGGG-TG--------GCGG-GCCCGAAAACCATTGGCGGTTC--GGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--G-CC-CGCCAGACAACCGAGAAACCCGATT-AT-CT-CAC---GATTGACC
		Ramalina_intermedia           AAAA-CTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-A-GCTTGGTATTGGGTC-CTTCGC---CGGGGG-TACTCCC-CGG-GGTGCCCGAAAAGCATTG-CGGTCC--GGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGCCTCGCA-C--C-GTGG-CC-GGCCAGACAACC-----C-CC-ATA-TTTCT-CAC---GATCGACC
		Ramalina_leptocarpha          AAAA-CTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-A-GCTTGGCATTGGGTCACT-CGC---CCAAA---AC-CAT-TGGCGG-GCCCGAAAACCATTGGCAGTCC--GGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-GA---CCTGGCCAGATAAA-----------ATA-AT----CAC---GATTGACC
		Lecanora_varia                AAAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCC-TCAAGC-TCA-GCTTGGTATTGGG-A-CTTCGC---CT-----T---CC-GAGGCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCG-T--C-GT-GACC-GGCCAGA--ACG-----CCCA-AAACTTT-TTCAA--TGATTGACC
		Lecanora_polytropa            AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGCGT-A-GCTTGGTATTGGG-C-CTCCGC---CC---------CC-GCGGCGG-GCCTGAAAGTCAGTGGCGGTCC--AGTGTGACTTCAAGCGTAGTAAA-AT-A-CCTCCCGC-TTTGGAAGCT-CGCG-A--C-GT-GGCC-GGCCAGA--ACG-----CCCA-A--CTTT-T-CAA--TGATTGACC
		Lecanora_contractula          AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-TCT-GCTTGGTATTGGG-C-CT-CGC---CC-----C---CGCG-GGTGG-ACCCGAAAGTCAGTGGCGGCCC--GGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT-TGGCGTC--CAG--G-CC-GGCCAGC---CA----GCCTTTTTA-TTT-T-CAA--TGATTGACC
		Lecanora_muralis              -AAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ACCCCTCAAGC-TCC-GCTTGGTATTGGG-T-CTTCGCT--CT-----T---CG-G-AGCGG-GCCCGAAAGTTAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC-TCGCG-C--C-GT-GACC-GGCCAGA--AC-----GCCCCAAT--TTT-T-CAA--TGATTGACC
		Ramalina_fraxinea             AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGC-ACCACTCAAGCGT-A-GCTTGGTATTGGGTC-CTTCGC---CCGGGG-T-CTCCCGCGGCGG-GCCCGAAAAGCATTGGCGGTCC--GGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--GCCC-GGCCAGACAACC-----CCCCAAT-CTT--T-CAC---GATTGACC
		Lecanora_glabrata             AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-T-CTGCTTGGTATTGGGCC-CT-CGC---CC----------CCGCGGCGT-GCCCGAAAATCAGTGGCGGCCC--GGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGC-TCCCG-CTGC-G--GCCC-G-CCAGA--ACC-----CCACAAA-CTT--TTCACAATGATTGACC
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 365 ; 
 CODESET * UNTITLED = Universal.ext: all ; 
 END;

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