NEXUS
[File created by TreeBASE:  7/26/07  20:56:08]
[Matrix accession#: M322]

BEGIN TAXA;
	TITLE M322;
	DIMENSIONS  NTAX=20;
	TAXLABELS
		Xenopus_laevis	Urechis_caupo	Sternaspis_scutata	Ridgeia_piscesae	Rhynchosciara_americana	Placobdella_parasitica	Pheretima	Onchocerca_volvulus	Nereis_virens	Cerebratulus	Mytilus	Lumbricus_terrestris	Listriolobus_pelodes	Lamellibrachia	Harmothoe_imbricata	Bombyx_mori	Axiothella_rubrocincta	Artemia	Apis_mellifera	Alvinoconcha_hessleri
	;
END;

BEGIN CHARACTERS;
	TITLE M322;
	DIMENSIONS NCHAR=345;
	FORMAT DATATYPE = DNA MISSING = . GAP = -  ;
	MATRIX
		Xenopus_laevis                AAGAACGTTTCCGTGAAGGACGTCCGTCGTGGCAACGTTGCTGGTGACAGCAAGATTGACCCACCAATGGAAGCTGGTTCTTTTACCGCACAGGTTATCATCCTGAATCACCCAGGCCAGATTGGTGCTGGATATGCCCCTGTGTTGGATTGCCACACTGCTCACATTGCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGATCGCCGTTCTGGTAAGAAACTGGAAGACAATCCCAAGTTCCTGAAGTCTGGAGATGCTGCCATTGTTGACATGATCCCAGGAAAGCCAATGTGCGTGGAGAGCTTCTCAGACTACCCTCCTCTTGGTCGTTTTGCTGTCCGT
		Urechis_caupo                 AAGAACGTTTCTGTCAAGGAAATCCGCAGAGGGTATGTTGCTGGCGATTCCAAGAATGATCCACCCAAGGCCACTGAAAACTTCAAGGCCCAGGTGATCATCCTGAACCACCCYCSCAGCATCTCCAGTGGATACCCCCCGGTGTTGGATYSCCACACCGCYCACATAGCCTGCAAGTTCCAGGAGATCCTTACCAAGAGTGGTCGTCGTACTGGCAAGACCCTTGAAGAGAACCCCCAGGCCGTCAAGTCTGGCGATGCCTGCATGGTAAACATGGTGCCCCAGAAGCCCATGTGTGTTGAGGCTTTCAACGACTACGCTCCCCTGGGACGTTTTGCCGTGCGT
		Sternaspis_scutata            AAGAACGTCTCTGTCAAAGACATCCGTCGAGGATACGTTGCCGGCGATTCAAAGAATGACGCTCCCAAGGAAGCGCAGGAATTCAAGGCTCAGGTTATTATCCTGAATCACCCTGGTCAGATTAACGCCGGGTATGCGCCGGTGCTGGACTGTCACACAGCTCATATCGCCTGCAAGTTCAGGGAGCTGGTCGAGAAGATTGATCGTCGTAGTGGAAAGTCTCTGGAGACTAGCCCCAGCAGCATTAAATCTGGTGAGGCCGCCATCGTTAACATGGTGCCCCAAAAGCCAATGTGTGTCGAGACCTTCAATGAATACGCCCCTCTTGGACGTTTTGCCGTTCGT
		Ridgeia_piscesae              AAGAACGTGTCCGTCAAGGATGTCCGTCGAGGCTTCGTGTGTGGTGACTCGAAGAACGACCCACCAATGGAGACAGATGAATTCCTTGCTCAGGTGATCATCCTGAACCACCCAGGTACGATCCAGGCTGGATACGCACCCGTCCTCGACTGCCACACGGCCCACATTGCGTGCAAGTTCAAGGAGCTGAAGGAGAAGATCGATCGCCGTAGCGGAAAGGTGCTCGAGGCCAACCCCCAGAGCGTGAAGTCTGGCGACGCCGCGATGGTTGAA........................................................................
		Rhynchosciara_americana       AAAAACGTTTCCGTCAAGGAATTGCGTCGTGGTTACGTTGCTGGTGACTCGAAAGCCAATCCGCCAAAAGGAGCCGAAAACTTCACCGCACAAGTCATCGTTCTTAATCACCCCGGACAAATCTCTAACGGTTACACTCCCGTCTTGGATTGTCACACTGCTCACATTGCATGCAAATTCGCCGAAATTAAGTA.AAGGTTGACCGTCGTTCAGGTAAATCAACTGAAGACAATCCAAAAGCCATCAAGTCTGGTGATGCTGCCATTGTCATCCTTCAACCATCCAAACCGTTGTGTGTCGAGTCCTTCCAAGAATTCCCACCATTGGGACGTTTTGCCGTTCGA
		Placobdella_parasitica        AAAAATGTGTCTGTTAAAGATATTAGGCGTGGGAATGTTGCCGGTGATTCCAAAAATGATCCACCAAAAGAAACTGAAGAATTCAAAGCTCAAGTTATTATTATGAACCATCCTGGCCAAATCAGTGCTGGTTATGCCCCAGTGGTCGACTGTCATACTTCTCATATTGCTTGTAAATTCCGTGATTTGTTGGAGAAGATTGATCGTCGTAGTGGGAAAAAGCCAGAGGACAACCCCGCCAATGTTAAAGCTGGAGACGCTGCTATAGTTGAAATGGTCCCACAAAAACCAATGTGTGTGGAATCATTTTCTGAATATCCTCCTTTA.GTCGTTTTGCCGTTCGT
		Pheretima                     AAGAACGTGTCGGTGAAGGACATCCGCCGTGGTAATGTTGCCGGAGACTCGAAGAATGATCCTCCTAAGGAGACTGAGGAATTCAAGGCACAGGTTATCATTCTGAACCATCCAGGACAGATCAATGCTGGTTATGCCCCAGTCGTTGACTGCCACACCTCGCACATTGCCTGCAAATTCCGCGAGCTGCTGGAGAAGATCGACCGTCGTAGCGGAAAGAAGCTGGAAGACAATCCTGCCAACGTCAAGTCCGGAGATGCCGCCATCGTCGAGATGGTTCCTCAGAAGCCGATGTGCGTCGAGGCGTTCTCCGACTACGCGCCGCTGGGAAGATTTGCCGTGCGC
		Onchocerca_volvulus           AAAAATATCTCTATTAAGGACATCCGACGTGGATCGGTAGCATCTGATTCTAAAAATGATCCGGCTAAAGAAACCAAAATGTTCACTGCCCAGGTCATTATTATGAATCATCCGGGCCAAATTTCTGCTGGATACACTCCTGTGCTTGATTGTCATACCGCTCACATTGCTTGCAAATTTGCGGAACTCAAAGAAAAAGTTGATCGAAGATCTGGTAAAAAAGTGGAGGACAATCCAAAGTCACTAAAGTCTGGTGATGCCGGTATTATCGATCTGATACCAACTAAACCACTATGTGTCGAAACTTTCACTGAGTATCCACCATTGGGACGATTTGCTGTGCGT
		Nereis_virens                 AAGAACATCTCTGTCAAGGACATCCGTCGTGGAAACGTTGCGTCCGACAGCAAGAATGACCCCGCCAAGGAGACTGAAGACTTCAAGGCTCAGGTCATCATCCTGAACCACCCCGGAGAGATCCGTGCTGGCTACGCCCCTGTGGTTGATTGCCACACAGCTCACATTGCTTGCAAGTTCGCTGACCTGAAGGAAAAGATTGATCGTCGTTCCGGTAAGAAGCTGGAAGACAACCCCGAGAAGGTCAAGTCTGGAGATGCCGCCATTGTGCGCATGGTTCCACAGAAACCCATGTGTGTCGAGGS.TTTTCAGACTACGCTCCCCTCGGACGTTTTGSCGTTCCG
		Cerebratulus                  AAGAACGTTTCTGTAAAGGAGATCAAGCGAGGGATGGTCGCTGGTGACAACAAGAACGATCCTCCAAAAGGTTGCGAAAACTTCACAGCACAGGTTATTATTCTCAATCATCCCGGAGAGGTCCACGCTGGTTATTCGCCGGTACTCGATTGCCACACTGCTCACATTGCGTGTAAATTCCTCGAATTCAAGGAAAAGATCGACAGGAGGAGTGGCAAGAAGCTAGAGGATAACCCCAAGATGGTCAAGTCGGGAGATGCCGCTATTGCCGTGCTCCAGCCGAGCAAGCCTATGGTAGTCGAATCGTTCGTCGACTATCCTCCGCTAGGAAGGTTTGCTGTGCGC
		Mytilus                       AAGAACGTCTCCGTCAAGGAAATTCGTAGAGGAATGGTCTGTGGTGACAGCAAAAATGACCCACCCAAAGGAGCCAAAAGCTTTATTGCACAGGTCATCATCTTGAACCACCCTGGAGAAATTAAGAATGGATATGCGCCAGTCTTGGATTGTCATACAGCTCATATTGCCTGTAAATTTGTTGAAATCAAAGAAAAGATTGACAGAAGAAGTGGTAAGAAACTTGAAGAATTCCCAAAATTCATCAAATCTGGGGATGCTGGTATTGTGGACATGACACCATCAAAGCCTATGTGTGTTGAATCCTTCCAAACATACGCCCCATTAGGACGTTTTGCTGTAAGA
		Lumbricus_terrestris          AAGAACGTGTSGGTGAAGAACATCCGTCGTGGTAACGTTGCTGGCGACTCCAAGAATGATCCTCCAAAGGAGACTGAAGAATTCAAAGCACAGGTTATCATTCTGAACCATCCAGGACAGATCAACGCTGGTTATGCGCCAGTTGTTGACTGCCACACCTCGCACATCGCCTGCAAATTCCGAGAGCTGCTGGAGAAGATCGACGGTGGTAGCGGAAAGAAGCTGGAAGACAACCCTGCCAACGTCAAGTCCGGAGACGCCGCCATCGTCGAGATGGTTCCCCAGAAGCCAATGTGCGTCGAGGCTTTCTCCGACTACGCCCCGCTGGGAAGATTCGCCGTGCGT
		Listriolobus_pelodes          AA.AACGTCTCCGTCAAAGAAATCCGAA.AGGATATGTGGCCGGCGACTCCAA.AATGATGCCCCCAAGGTCTGCGACAGCTTCAAGGCCCAGGTTATCATTCTGAACCACCCTGGCACCATCAGTGCTGGCTATGCCCCAGTGTTGGATTGTCATACCGCTCACATCGCCTGCAAGTTCGGGGAAATTCTGGCCAA.ATGGACCGTCGTTCCGGCAAGACCCTTGAA.A.AACCCCAAGGATCT.GAATCTGGTGATGCCAGTATGGTGAACATGGTGCCCCA.AAACCCATGTGTGTGGA.CCTTTCTCTGATTACGCACCTCTCGGACGCTTTGCTGTGCGT
		Lamellibrachia                AAGAATGTGTCTGTCAAGGACATCCGTCGTGGTTTCGTGTGCGGTGACTCAAAGAACGATCCTCCCCTGGAGACTGACGAGTTCCTTGCTCAGGTGATCATCCTGAACCACCCCGGAACGATCCAGGCTGGATACGCCCCCGTGCTCGACTGCCACACAGCCCACATTGCGTGCAAGTTCAAGGAGCTGAAGGAGAAGATTGATCGTCGTAGCGGCAAAGTGCTTGAGGCCACCCCCCAGAGCGTGAAGTCTGGTGATGCTGCCATGGTCGAGATGATACCCCAGAAGGCCATGTGCGTTGAGAAGTTCTCCGAGTATGCCCCACTTGGTCGCTTTGCCGTCCGT
		Harmothoe_imbricata           AAGTCTGTGTCAGTCAAGGACATACGACGTGGAAACGTCGCCGGTGACAGCAAGAACGACCCTCCCAAGGAGGCTAAGGAGTTCAACGCTCAGGTCGTCATCCTGAACCACCCTGGCCAGATCAACGCCGGGTACGCACCTGTGGTCGATTGCCACACTGCCCACATTGCCTGCAAGTTC.CCGAGCTGATCGAGAAGATCGATCGTCGTTCCGGCAAGAAGCTCGAGGACAACCCCAACCACGTCAAGTCTGGTGACGCC.CCATGGTCAAGATGGTGCCCCAGAAGCCCATGTGCGTGGAGGCCTTCTCCGACTACCAGCCCCTCGGACGTTTCGCCGTCCGT
		Bombyx_mori                   AAGAACGTGTCCGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACTCCAAAAACAACCCACCTAAGGGTGCTGCAGATTTTACAGCTCAAGTCATTGTGCTTAACCATCCTGGTCAAATCTCAAACGGTTACACACCAGTCTTGGATTGCCACACTGCCCACATTGCCTGCAAATTTGCAGAAATCAAAGAAAAAGTTGACCGTCGTACTGGTAAATCTACTGAAGTCAACCCAAAATCCATCAAGTCTGGAGATGCAGCCATTGTCAACTTGGTACCTTCCAAGCCTCTATGTGTAGAGTCCTTCCAGGAATTCCCACCCCTCGGTCGTTTTGCTGTCCGT
		Axiothella_rubrocincta        AAGAACGTGTCCATCAAGGATATCCGTCGTGGCAACGTCTGCGGAGACTCCAAGAATGATCCGCCCTCTGCAAGCTCGGAATTCAATGCCCAGGTGATCATCCTGAACCACCCTGGTGAAATCCATGCTGGATACTCTCCAGTCGTAGACTGCCACACTGCCCACGTTGCCTGCAAATTCAGTGAGCTAAAGGAGAAAATAGACCGTCGTAGTGGCAAGAAGCTAGAAGACAACCCGAAAATGGTAAAATCTGGAGATGCCTGCATCGCGGTTTTGGTGCCCAGCAAGCCCATGTGTGTCGAGGCTTTCTCAAACTACCCTCCCCTGGGACGTTTTGCCGTGCGC
		Artemia                       AAAAACGTTTCAGTCAAAGAACTTCGTCGTGGCTACGTCGCCTCAGATTCAAAGAACAATCCAGCCAGAGGCTCTCAAGATTTCTTTGCTCAGGTTATTGTCTTGAACCACCCTGGTCAGATCTCAAACGGTTACACTCCTGTCTTGGACTGCCACACAGCTCACATTGCTTGCAAGTTTGCTGAGATTAAAGAGAAGTGTGACAGACGTACTGGCAAAACAACTGAAGCTGAGCCAAAATTTATCAAGTCAGGTGATGCGGCCATGATCACTTTGGTACCTTCCAAGCCGTTGTGTGTTGAAGCCTTTTCCGACTTCCCACCTCTTGGTCGATTTGCTGTCCGT
		Apis_mellifera                AAGAACATTTCTGTGAAAGAGTTGAGGCGTGGTTACGTGGCGGGAGATTCGAAAAATCAACCGCCACGGGGGGCAGCCGATTTCACAGCGCAGGTGATCGTCCTCAATCATCCTGGGCAGATAAGCAACGGTTATACACCGGTGCTCGATTGTCACACCGCTCATATCGCTTGCAAATTTGCGGAGATCAAGGAGAAATGCGACCGCCGTACCGGCAAGACCACCGAGGAGAATCCGAAGAGCATCAAGAGCGGAGACGCCGCGATCGTGATGTTGCAACCTACTAAGCCGATGTGCGTCGAAGCTTTCCAGGAATTCCCTCCGCTTGGTCGCTTCGCGGTTCGC
		Alvinoconcha_hessleri         AAGAACATCTCTGTCAAGGATATTCGCCGTGGCAACGTGGCTGGTGACACGAAGAACGACCCCCCCAAGGAATGCAAGAGCTTCTATGCCCAGGTCATCATCCTCAACCACCCTGGTGAGATCAAGGCTGGCTATGCACCAGTGTTGGATTGCCACACCGCTCACATCGCCTGCAAGTTTTCTGAGCTGAAAGAGAAGTGTGACAGGCGTTCTGGCAAGAAGCTGGAAGACAACCCCAAATCTGTGAAGACCGGTGATGCTGCCATGGTGGACCTGGTCCCCAGCAAGCCAATGTGCGTAGAGGCCTTCTCAGAGTACCCACCTCTGGGTCGGTTTGCTGTCCGC
	;
END;

BEGIN CODONS;
CODESET * UNTITLED = mtDNA.mam.ext: all ; 
 END;

BEGIN ASSUMPTIONS;
USERTYPE a STEPMATRIX = 4 
 A C G T 
 . 4 1 4 
 4 . 4 1 
 1 4 . 4 
 4 1 4 . 
 ; 
 
 OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 CHARSET first = 1 - 340 \ 3 ; 
 CHARSET second = 2 - 344 \ 3 ; 
 CHARSET third = 3 - 345 \ 3 345 ; 
 TYPESET user_a = a: 1 - 345 ; 
 END;