NEXUS
[File created by TreeBASE:  7/26/07  21:01:55]
[Matrix accession#: M1387]

BEGIN TAXA;
	TITLE M1387;
	DIMENSIONS  NTAX=21;
	TAXLABELS
		Anthothela_nuttingi	Paramuricea_sp	Protodendron_sp	Lophogorgia_chilensis	Leptogorgia_virgulata	Muricea_fruticosa	Acanthogorgia_sp	Anthomuricea_sp	Alcyonium_sp	Sarcophyton_glaucum	Corallium_kyshinouyei	Corallium_ducale	Paragorgia_sp	Chrysogorgia_cryseis	Isidid_A	Isidid_B	Narella_bowersi	Narella_nuttingi	Isidella_sp	Lepidisis_olapa	Renilla_muelleri
	;
END;

BEGIN CHARACTERS;
	TITLE M1387;
	DIMENSIONS NCHAR=524;
	FORMAT DATATYPE = RNA MISSING = ? GAP = -  ;
	MATRIX
		Anthothela_nuttingi         CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACUUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Paramuricea_sp              CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCAAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACUUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAAAUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCUUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAG----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Protodendron_sp             CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACUUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Lophogorgia_chilensis       CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACCUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUAGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Leptogorgia_virgulata       CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACCUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU-CGGGCGAUAAUGACCCGAUAUGAUAGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Muricea_fruticosa           CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACUUAAAAUGAUCGAUACAAAGUAUCCUAAUUUUGAGUUAAUAAAUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUAUAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Acanthogorgia_sp            CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCAAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCUAUAGCGUUAACUUAAAAUGAUCUAUACUAAGUAUUCUAAUUUUGAGUUAAUAAAAUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCUUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAG----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCGAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Anthomuricea_sp             CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACCUAAAAUGAUCGAUACUAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGCUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGAC-UAC----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUGAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Alcyonium_sp                CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGAUCUUACUGUCUCAAGAGAAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAGAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAACUUAAAAUGAUCGAUA-UAAGUAUCCUAAUUUUGAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUACAA-AGC-UAUCACAUUAGCCUGACAGUGAGGGGGACAUCCCUAGCUGGCACAAGGAC--AA----------------------------------------------------------------------GUCCUAUGU--GGGCGAUAAUGACCCGAUAUUAUUGUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Sarcophyton_glaucum         CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAAUCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAGUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUGUCGAGCUUUACUGGAUACCGAUAGUGUUAACUUAAAAUAAUCGAUACUAUGUAUCCUGAUUUUGAGUUAAUAAUUUUUGUUGGUAAGACAGUUUAGUUGGGGCGACUACCUUUGAUUAAGAAACGAAGGCAAGCUUAUGGUGUAUUUUAGUUAAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGCCACAAG---------------------------------------------------------------------------------AAUGUG-GGGCGAUAAUGACCCGAUAUGAUCAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGCAGGG
		Corallium_kyshinouyei       CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACACAAACAUUGUAAGACGAAAAGACCCUGUCGAGCUUUACUGGAUACCAAUAGCGUUAAUUUAGAAUGAUCGGUACUAAGUAUUCUAAUUUUAAGUUAAUAAUUUUUGUUGGCAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-AA--AAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGACCUACUCGUAUAGUAUAU----------------------------------------UAUAUAUACGUAAUGGC-UCCUAUGU--GGGCGAUAAUGACCCGAUAUAAUUUUCCUCAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGCAGGG
		Corallium_ducale            CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGAAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUGUCGAGCUUUACUGGAUACCAAUAGCGUUAAUUUAGUAUGAUCGGUACUAAGUAUUCUAAUUUUAAGUUAAUAAUUUUUGUUGGCAGGACAGUUUAGUUGGGGCGACUACCUCUGAAUAGGAAACGAAGGCGAGCUUAUGGUGUUAUU-AA--AAUCUCAUUAGCCUGACAGUGAGGGGAACACCCCUAGCUGGCACAGGGACUUACCCAUUUA---------------------------------------------------CAACGUAAUGGGAUCCUAUGU--GGGCGAUAAUGACCCGAUAUAAUUAUCCUGAAUAUAUAUCGAAAGCGGAUAAAAGCUACCGCAGGG
		Paragorgia_sp               CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUGUCGAGCUUUACUGGAUACCAAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUUCUAAUUUUAAGUUAAUAAUUCUUGUUGGCAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUUUAA--AAUCUCAUUAGCCUGACAGUGAGGGGGACACCCCUAGCUGGCACAAGGACCUACCCACCUAGUAUAU----------------------------------------AAUAUAUACGAAAUGGGUUCCUAUGU--GGGCGAUAAUGACCCGAUAGAAUUAUCCAAAUUAAAUAUCGAAAGCGGAUAAAAGCUACCGCAGGG
		Chrysogorgia_cryseis        CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGAAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGGAUGGUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-AA--AAUCUCAUUAGCCUCACAGUAAGGGGGAUACCCCUAGCUGGCACAAGGACUUACCCACAUAGUAU-CUUCGCCCCUUUGGGGGGGGAG------------------------AUACGUAAUGGGUUCCUAUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Isidid_A                    CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-AA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACAGGCCCU------CAUAGUAUA------------------------------------------UUAUAUGCGGAA-GGG-----AUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Isidid_B                    CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUUUAA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACA--------CCCCAAAAGGACAUUUGUCCCCC-------------------------------------AACGUAA-GGG-----AUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Narella_bowersi             CUGAAUGGCCGCGGUAACUCUGACCGCGAUAAUGUAGCACAAUAAAUAGCCA-UUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-GA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACAAGGACUUACCCACAUAGUAUAU----------------------------------------AGUAUAUACGUAAUGGGUUCCUAUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Narella_nuttingi            CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAGACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUCGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-GA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACAAGGACUUACCCACAUAGUAUAU----------------------------------------AUUAUAUACGUAAUGGGUUCCUAUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Isidella_sp                 CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-AA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACAAGCCCGUA---ACAUAGUAA-----------------------GGGCAAGGGAACUUAGCCCGUU------CUAUGGGG-----AUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Lepidisis_olapa             CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGGGUAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGGAAAGCCGAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAGCGUUAAUUUAGAAUGAUCGAUACUAAGUAUCCUAAUUCUAAGUUAAUAAUUUUUGUUGGUAGGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAUU-AA--AAUCUCAUUAGCCUCACAGUGAGGGGGACACCCCUAGCUGGCACA----CGUA------------------------------------------------------------------AAGGG-----AUGU--GGGCGAUAGUGACCCGAUAUGAUUAUCCAAAAUAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
		Renilla_muelleri            CUGAAUGGCCGCGGUAACUCUGACCGUGAUAAUGUAGCACAAUAAAUAGCCAAUUAAUUGUUGGCGG-UAUGAAUGGAACCACGAGGGUCUUACUGUCUCAAGAGAAAAGCCAAUGAAAUUAUAAUUGUAGUGAAGAUACUACAUAAACAUUGUAAGACGAAAAGACCCUAUCGAGCUUUACUGGAUACCGAUAACGUUAACUUAGAAUGAUCGAUACUAAGUACCCUAAUUCUAAGUUAAUAAAUUUUGUUGGUAAGACAGUUUAGUUGGGGCGACUACCUUUGAAUAAGAAACGAAGGCGAGCUUAUGGUAUUAAU-AA--AAUCUCAUUAGCCUCACAGUGAGGA--ACACCCCUAGCUGACACAAGGACCU---------------------------------------------------------------CGCUA-GGGUUCCUAUGU--GGGCGAUAGUGACCCGAUAUUAUUAUCCAAAAGAAAUAUCGAAAGCGGAUAAAAGCUACCGUAGGG
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 524 ; 
 CODESET * UNTITLED = Universal: all ; 
 END;

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