NEXUS
[File created by TreeBASE:  7/26/07  20:58:22]
[Matrix accession#: M790]

BEGIN TAXA;
	TITLE M790;
	DIMENSIONS  NTAX=13;
	TAXLABELS
		Ramalinora_glaucolivida	Lecanora_garovaglii	Lecanora_contractula	Lecanora_muralis	Lecanora_polytropa	Lecanora_varia	Ramalina_sinensis	Ramalina_montagnei	Ramalina_menziesii	Ramalina_intermedia	Ramalina_leptocarpha	Ramalina_fraxinea	Lecanora_glabrata
	;
END;

BEGIN CHARACTERS;
	TITLE M790;
	DIMENSIONS NCHAR=350;
	FORMAT DATATYPE = DNA MISSING = ? GAP = -  ;
	MATRIX
		Ramalinora_glaucolivida       AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACCCTCAAGCGTAAGCTTGGTATTGGGTC-TTCGCCGTCCCCCTCGGGGGGTGGCGGGCCCGAAAGACAGTGGCGGTCCCCGGGGATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGAAC-CGTTTGGAG-CCGGCCAGACAAC----------AAAAATT--TCTAT--GATT----
		Lecanora_garovaglii           AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC
		Lecanora_contractula          AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCC-T-CGC-C-------C-CCGCGG-GTGGACCCGAAAGTCAGTGGCGGCCCGGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT--TGGCGTCCAGGCCGGCCAGCCAGCC-------TTTTTA-TT-TTCAAT--GATTGACC
		Lecanora_muralis              -AAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACACCCCTCAAGCTCC-GCTTGGTATTGGGTC-TTCGCTC-------T-TCG-GA-GCGGGCCCGAAAGTTAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC--TCGCGCCGTGACCGGCCAGAACGCC-------CCAAT--TT-TTCAAT--GATTGACC
		Lecanora_polytropa            AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCGTA-GCTTGGTATTGGGCC-TCCGCCC---------CCGCG--GCGGGCCTGAAAGTCAGTGGCGGTCCAGTGTGACTTCAAGCGTAGTAAA-AT-A-CCTCCCGC-TTTGGAAGC--TCGCGACGTGGCCGGCCAG--AACG-------CCCAACTTT--TCAAT--GATTGACC
		Lecanora_varia                AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC
		Ramalina_sinensis             AAAACTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTTCTTCGCCCGGGG-TCTCCCGCG--GCGTGCCCGAAAAGCATTGGCGGTCCGGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGC-CTCGCCCCGGGTCCGGCCAGACAACC-----CCCACATATAT-CTCAC---GATTGACC
		Ramalina_montagnei            AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTTTTTCGCCGGGGGCTTTTCCCCA--GCGTGCCCGAAAAGCATTGGCGGTCCGGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGC-CTCGTGCTGTGGCCGGCCAGACAACC-----CCCCCAT--AT-CTCAC---GATTGACC
		Ramalina_menziesii            AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCATTCGCCCGGGG-TG---------GCGGGCCCGAAAACCATTGGCGGTTCGGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG--GCCCGCCAGACAACCGAGAAACCCGATT-AT-CTCAC---GATTGACC
		Ramalina_intermedia           AAAACTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCGGGGG-TACTCCCCG--GGGTGCCCGAAAAGCATTG-CGGTCCGGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGC-CTCGCACCGTGGCCGGCCAGACAACC-----C--CCATA-TTTCTCAC---GATCGACC
		Ramalina_leptocarpha          AAAACTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCACTCGCCCAAA---AC-CATTG--GCGGGCCCGAAAACCATTGGCAGTCCGGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCGAC-CTGGCCAGATAAA-----------ATA-AT---CAC---GATTGACC
		Ramalina_fraxinea             AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCCGGGG-TCTCCCGCG--GCGGGCCCGAAAAGCATTGGCGGTCCGGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG-GCCCGGCCAGACAACC------CCCCAATCTT-T-CAC---GATTGACC
		Lecanora_glabrata             AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCCCT-CGCCC---------CCGCG--GCGTGCCCGAAAATCAGTGGCGGCCCGGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGCTCCCGCTGCG-GCCCG-CCAGA--ACC------CCACAAACTT-TTCACAATGATTGACC
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 350 ; 
 CODESET * UNTITLED = Universal.ext: all ; 
 END;

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