#NEXUS

begin data;
	dimensions  ntax=9 nchar=720;
	format datatype=rna interleave=no gap=- missing=?;
	matrix
	[       1   2   3   4   5   6   7   8   9   10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50]
	FR      GGC AAC GGU --- GUG UUU ACU GUU CCG AAG AAC AAU AAA AUA GAU CGG GCU GCU UGC AAA GAG CCU GAU AUG AAU AUG UAC UUA CAG AAA GGG GUC GGC GGU UUC AUC CGU CGC CGC CUU AAG ACU GUG GGU AUA GAC UUG AAC GAU CAA ACG AUC AAU CAA CGC CUG GCU CAA CAA GGU AGC CGU GAU GGG UCU UUG GCG ACG AUA GAC UUA UCG UCU GCU UCU GAC UCC AUC AGC GAC CGC CUA GUG UGG AGU UUU CUC CCA CCU GAG CUA UAU UCA UAU CUC GAC AUG AUU CGA AGC CAC UAC GGU UAC GUA --- AAU GGC AAG AUG AUU CGU UGG GAA CUA UUU UCG ACG AUG GGU AAU GGG UUC ACC UUU GAA CUA GAG UCC AUG AUU UUC UGG GCU AUA GUC AGG GCU ACU CAG AUC CAU UUU CGU --- AAC ACC GGA ACC AUU GGC AUC UAU GGG GAC GAU AUU AUA UGC CCC ACA GAG AUU GCA CCU CGC GUG CUG GAA GCA CUG AGC UUC UAC GGU UUC AAA CCG AAU CUA CGA AAG ACG --- UUC ACG UCC GGC UCU UUU CGC GAG AGC UGC GGC GCG CAC UAU UUC CGU GGU GUC GAU GUU AAA CCA UUU UAU AUC AAG AAA CCA AUC ACU GAC CUA UUC UCC CUA AUG CUU AUA CUU AAC CGU AUA CGC GGA UGG GGG GUA GUC AAC GGA AUAGCAGACCCACGCCUC
	MS2     GGG AAC GGA --- GUG UUU ACA GUU CCG AAG AAU AAU AAA AUA GAU CGG GCU GCC UGU AAG GAG CCU GAU AUG AAU AUG UAC CUC CAG AAA GGG GUC GGU GCU UUC AUC AGA CGC CGG CUC AAA UCC GUU GGU AUA GAC CUG AAU GAU CAA UCG AUC AAC CAG CGU CUG GCU CAG CAG GGC AGCGUAGAUGGUUCGCUUGCGACGAUAGACUUAUCGUCUGCAUCCGAUUCCAUCUCCGAUCGCCUGGUGUGGAGUUUUCUCCCACCUGAGCUAUAUUCAUAUCUCGAUCGUAUCCGCUCACACUACGGA---GUA---GAUGGCGAGACGAUACGAUGGGAACUAUUUUCCACAAUGGGAAAUGGGUUCACAUUUGAGCUAGAGUCCAUGAUAUUCUGGGCAAUAGUCAAAGCGACCCAAAUCCAUUUUGGU---AACGCCGGAACCAUAGGCAUCUACGGGGACGAUAUUAUAUGUCCCAGUGAGAUUGCACCCCGUGUGCUAGAGGCACUUGCCUACUACGGUUUUAAACCGAAUCUUCGUAAAACG---UUCGUGUCCGGGCUCUUUCGCGAGAGCUGCGGCGCGCACUUUUACCGUGGUGUCGAUGUCAAACCGUUUUACAUCAAGAAACCUGUUGACAAUCUCUUCGCCCUGAUGCUGAUAUUAAAUCGGCUACGGGGUUGGGGAGUUGUCGGAGGUAUGUCAGAUCCACGCCUC
	GA      GGC AAC GGU --- UUG UUU UCU GUU CCG AAG AAC AAU AAA AUA GAU CGG GCU GCC UGU AAG GAG CCU GAU AUG AAU AUG UAC CUU CAG AAG GGG GCG GGA UCU UUU AUA AGA AAA CGC CUU CGC UCC GUC GGU AUA GAU CUU AAC GAU CAG ACG CGC AAU CAG GAA UUA GCC CGA CUU GGC AGCAUUGAUGGUUCGCUCGCUACUAUUGAUCUUAGUAGCGCUAGCGAUUCCAUCUCUGACCGUCUUGUCUGGGAUCUACUUCCGCCGCACGUUUAUUCAUACCUCGCUCGUAUCCGAACAUCGUUCACUAUGAUC---GAUGGGCGUUUACAUAAGUGGGGUCUAUUUUCUACCAUGGGUAAUGGCUUCACGUUCGAACUCGAGUCCAUGAUCUUUUGGGCUUUAAGCAAGAGCAUUAUGCUGUCCAUGGGUGUU---ACUGGCUCAUUAGGCAUCUACGGUGAUGAUAUAAUCGUCCCCGUUGAGUGUCGUCCAACUCUCCUUAAGGUACUAUCCGCUGUAAACUUUCUUCCUAAUGAGGAGAAAACA---UUUACAACGGGUUACUUUCGUGAAAGUUGUGGUGCCCACUUCUUCAAAGAUGCCGACAUGAAACCUUUUUACUGCAAGCGGCCAAUGGAAACCCUUCCCGAUGUCAUGUUGCUAUGCAACAGGAUAAGAGGUUGGCAGACCGUUGGUGGAAUGUCAGAUCCGCGACUC
	SP      UCA --- AAU AAA GCA GUC ACU GUU CCA AAG AAC AGU AAA ACU GAU CGC UGU AUU GCU AUC GAG CCC GGC UGG AAU AUG UUU UUC CAG UUA GGC GUC GGU GCA GUG CUA CGC GAU AGG UUG CGU UUA UGG AAG AUU GAU CUU AAU GAC CAA UCG ACC AAU CAA CGC CUC GCG CGU GAU GGG UCUCUGCUAAAUCAUUUAGCUACCAUAGACUUAUCUGCAGCCAGCGAUUCAAUCAGCCUUAAGCUUGUUGAGUUGCUCAUGCCCCCUGAAUGGUAUGACCUUCUAACGGAUCUCCGAUCCGAUGAAGGAAUACUGCCUGACGGGCGAGUUGUGACCUAUGAGAAAAUAUCCUCCAUGGGUAAUGGCUACACUUUCGAACUCGAGUCGCUUAUUUUUGCGGCUAUCGCUCGAAGUGUGUGCGAGUUACUGGAAAUUGACCAAUCUACUGUUAGCGUGUACGGGGAUGAUAUAAUCAUCGAUACCCGUGCCGCAGCUCCAUUAAUGGAUGUCUUUGAGUACGUCGGGUUCACUCCUAACAGAAAGAAAACG---UUCUGCGAUGGACCCUUCCGCGAAUCGUGCGGUAAGCACUGGUUCCAAGGGGUAGAUGUAACGCCCUUUUACAUACGACGACCAAUACGUUGCCUAGCCGAUAUGAUACUUGUAUUAAAUAGUAUCUAUAGGUGGGGCACUGUUGAUGGCAUAUGGGAUCCUAGAGCA
	NL95    UCG --- AAU AAA GCA GUC ACU GUU CCA AAG AAC AGU AAA ACU GAU CGC UGC AUU GCU AUC GAG CCC GGC UGG AAU AUG UUU UUC CAG UUA GGC GUC GGU GCU GUG CUC CGU GAU CGG UUG CGC CUU UGG CAU AUU GAU CUC AAU GAU CAA UCU GUU AAU CAG CGC CUC GCA CGU GAU GCA UCGCAGUUGGACCAUUUGGCCACUGUCGAUUUAUCAGCAGCAAGCGAUUCGAUAAGCUUACGGCUUGUUGAACUGCUAAUGCCGCCUGCUUGGUUUGAUCUCCUGACCGAUCUCCGAUCGGACCAGGGAAUCCUGCCUGACGGGCGUGUCGUUACUUACGAGAAAAUAUCCUCCAUGGGUAAUGGCUACACUUUUGAGCUAGAGUCGUUAAUUUUCGCGGCUCUCGCCAGAAGUGUGUGCGAGUUAUUGGACCUUGACCAGUCAACUGUCAGCGUGUACGGUGAUGAUAUAAUCAUCGAUUCACGUGCCGCUGAUGUCCUUAUGGCGGUUUUCGAGUAUGUUGGGUUUACGCCUAAUCGAAAGAAAACU---UUCAUUAAGGGCCCCUUUAGAGAGUCGUGCGGAAAGCACUGGCACUCCGGGGUUGACGUAACGCCCUUUUACAUACGCCGCCCAAUCCGCUGCCUAGCCGACAUGAUACUUGUAUUGAACAGUAUCUACCGGUGGGGUACGAUUGACGGUGUGUGGGAUCCUAGGGUA
	M11     CCU UUC AAU AAA GCA GUU ACU GUA CCA AAG AAC AGU AAA ACU GAU CGC UGU AUA GCC AUC GAA CCU GGC UGG AAU AUG UUU UUC CAG CUA GGU AUC GGU GGU GUU AUA CGC GAA AAG UUG CGU UUG UGG GGC AUC GAU CUG AAU GAU CAG ACG AUU AAC CAA ACG CGC GCA UAU UUA GGC AGCCGUGAUGAUAAUCUCGCCACGGUGGAUCUCUCAAGAGCUAGCGAUACUAUUUCGCUUGCCCUUGUUGAGCUCCUUAUGCCUCCUGAGUGGUUUAAGGUCCUGUUGGCCUUAAGAUCACCCAAGGGCAUCUUGCCAGAUGGUACCGUCAUUACUUAUGAGAAAAUAUCCUCAAUGGGUAAUGGCUAUACCUUCGAGCUUGAGUCGCUUAUAUUUGCGGCUCUUGCUCGGUCUUUAUGCGAAUUACUGGGCUUACGACCGUCAGAUGUUACGGUCUAUGGCGAUGACAUAAUAUUGCCAUCAGACGCGUGCAGUCCUCUAGUUGAAGUUUUCUCCUAUGUUGGUUUUCGUACCAACAAGAAGAAAACG---UUUUCUAGUGGACCGUUCCGAGAGUCGUGCGGAAAGCACUACUUUUUGGGCGUUGACGUCACACCUUUCUACAUACGUCGCCGUAUAGUGAGUCCCUCCGAUCUCAUACUGGUUUUGAACCAGAUGUAUCGUUGGGCCACAAUUGACGGCGUAUGGGAUCCUAGGGUA
	MX1     CCU UUC AAU AAA GCA GUU ACU GUA CCA AAG AAC AGU AAA ACU GAU CGC UGC AUC GCU AUC GAG CCA GGC UGG AAU AUG UUU UUC CAG UUG GGC AUU GGU GGC GUA AUU CGC GAA AAG UUG CAC UUG UGG AAU AUC GAC CUG AAU GAU CAG ACG AUU AAC CAG GUG CGC GCA UAU UCA GGC AGCUGUAGCAAUGAACUUGCUACAGUGGAUCUCUCGAGCGCGAGUGAUACUAUUUCGCUUGCGCUCGUUGAGCUCCUGCUACCCCCUGCGUGGUUUAAAGUCCUUACGGACCUUAGGUCACGAAGGGGUAUGUUGCCAGACGGUAGAAUCAUUACCUAUGAGAAAAUUUCCUCAAUGGGUAACGGUUUCACCUUCGAGCUCGAGUCGCUUAUAUUUGCAGCUCUUGCUCGGUCUUUAUGCGAGUUACUGAACUUACAACCGUCGAGUGUCACGGUCUAUGGCGAUGAUAUUAUAUUGCCAUCAGACGCGUGCAGCUCGUUGAUUGAAGUUUUCUCCUACGUAGGUUUUAGAACCAACGAGAAGAAGACC---UUUUUCGACGGGCCGUUCCGAGAGUCGUGCGGAAAGCACUACUUUAUGGGCGUUGACGUCACACCUUUCUACAUACGCCACCGUAUAGUGAGUCCCUCUGAUCUCAUACUGGUUUUGAACCAGAUGUAUCGUUGGGCCACGAUUGAUGGCGUAUGGGAUCCUAGGGUA
	QB      CCU UUU AAU AAA GCA GUU ACU GUA CCU AAG AAC AGU AAG ACA GAU CGU UGU AUU GCU AUC GAA CCU GGU UGG AAU AUG UUU UUC CAA CUG GGU AUC GGU GGC AUU CUA CGC GAU CGG UUG CGU UGC UGG GGU AUC GAU CUG AAU GAU CAG ACG AUA AAU CAG CGC CGC GCU CAC GAA GGC UCCGUUACUAAUAACUUAGCAACGGUUGAUCUCUCAGCGGCAAGCGAUUCUAUAUCUCUUGCCCUCUGUGAGCUCUUAUUGCCCCUAGGCUGGUUUGAGGUUCUUAUGGACCUCAGAUCACCUAAGGGGCGAUUGCCUGACGGUAGUGUUGUUACCUACGAGAAGAUUUCUUCUAUGGGUAACGGUUACACAUUCGAGCUCGAGUCGCUUAUUUUUGCUUCUCUCGCUCGUUCCGUUUGUGAGAUACUGGACUUAGACUCGUCUGAGGUCACUGUUUACGGAGACGAUAUUAUUUUACCGUCCUGUGCAGUCCCUGCCCUCCGGGAAGUUUUUAAGUAUGUUGGUUUUACGACCAAUACUAAAAAGACU---UUUUCCGAGGGGCCGUUCAGAGAGUCGUGCGGCAAGCACUACUAUUCUGGCGUAGAUGUUACUCCCUUUUACAUACGUCACCGUAUAGUGAGUCCUGCCGAUUUAAUACUGGUUUUGAAUAACCUAUAUCGGUGGGCCACAAUUGACGGCGUAUGGGAUCCUAGGGCC
	PP7     GAC AGC --- CGG UUC GAU UUU GUC GCU AAG ACC GCG AAG GCG GUU CGC UUC AUC GCU AUG GAG CCA GAA CUU AAC AUG CUG CUG CAG AAA UCU GUA GGA GAC ACG AUA AGG GCU GCU CUG CGG AAA GCG GGU AUC GAU CUC AAU ACC CAG CGA CUA AAU CAA GAU CUU GCG UAC CAC GGA UCCGUUUUUCGGAAUCUCGGUACGAUAGAUCUGUCUAGCGCUUCCGAUACGUUAAGCAUUGAACUCGUGCGGCAGUACCUGCCGAAGCGGUUUCUCCGCUAUGUAUUGGAUCUCCGAACCCCCUACACGAGUGUA---GGUGGUAAGAAGCACAGGCUCGAGAAGGUCGCUUCGAUGGGCAACGGGUUCAUUUUUGAACUCCAGAGCCUCAUCUACGCAGCCUUCGCGCAUGCCAUGACGCUAGUAGUAGGAGGAAGAGAAUGCGACAUAGCCAUUUACGGCGAUGAUAUCAUCGUCAGUGAAUGCGUAGUAGAGCCUCUGAUGCAGUUCCUCGAAUGGCAUGGGUUCUGCCCCAAUCUCGAUAAGAGUUAUUGGGGAGGGGAUCCAUUCCGCGAGUCCUGCGGGAAGCACUACUUCGCUGGUCGCGACGUUACCCCUGUCUACGUGAAGGGGGCCCUGGAUAACCUACCUGCCCUUUUCCGUCUCUUCAACUCGUUGAAGCGAUGGGAGGAGCAAACAGGUAUCCGGAUCCCUGACACG
	;
end;

begin mrbayes;
	[The following line is useful for automatic execution with no
	 warnings issued before files are overwritten and automatic
	 termination of chains after the prespecified number of generations.]
	set autoclose=yes nowarn=yes;
	
	[The following block demonstrates how you can set up a model that
	 allows the third codon position to have gamma-distributed rate
	 variation with a different shape parameter than the first and 
	 second positions.]

	[First define character sets]
	charset first_pos  = 1-720\3;
	charset second_pos = 2-720\3;
	charset third_pos  = 3-720\3;
	
	[Define the partition]
	partition by_codon = 3:first_pos,second_pos,third_pos;
	
	[Select the partition]
	set partition=by_codon;
	
	[Set a GTR + gamma model for all partitions]
	lset nst=6 rates=gamma;

	[This is the line that allows the gamma shape parameter of the third codon position
	 to be unique:]
	unlink shape=(3);
end;
