
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:28 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip" (19 taxa, 747 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRG	44	-3466.8958	7027.4326	0.5078	0.5078
HKYG	40	-3472.1095	7028.8648	0.2482	0.7560
GTRIG	45	-3466.9063	7029.7185	0.1619	0.9179
HKYIG	41	-3472.1097	7031.1046	0.0810	0.9989
GTRI	44	-3473.2482	7040.1373	0.0009	0.9998
HKYI	40	-3479.2442	7043.1342	0.0002	1.0000
K2PG	37	-3506.9957	7091.9576	0.0000	1.0000
K2PIG	38	-3506.9957	7094.1778	0.0000	1.0000
SYMG	41	-3505.5344	7097.9539	0.0000	1.0000
SYMIG	42	-3505.5345	7100.1996	0.0000	1.0000
K2PI	37	-3515.5786	7109.1233	0.0000	1.0000
SYMI	41	-3514.1518	7115.1886	0.0000	1.0000
HKY	39	-3529.1859	7140.7848	0.0000	1.0000
GTR	43	-3525.5507	7142.4841	0.0000	1.0000
K2P	36	-3561.8763	7199.5047	0.0000	1.0000
SYM	40	-3559.0538	7202.7535	0.0000	1.0000
F81G	39	-3570.1809	7222.7749	0.0000	1.0000
F81IG	40	-3570.1810	7225.0079	0.0000	1.0000
F81I	39	-3576.3947	7235.2024	0.0000	1.0000
JC69G	36	-3595.8174	7267.3869	0.0000	1.0000
JC69IG	37	-3595.8174	7269.6010	0.0000	1.0000
JC69I	36	-3602.9890	7281.7301	0.0000	1.0000
F81	38	-3621.5738	7323.3340	0.0000	1.0000
JC69	35	-3646.1443	7365.8330	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3466.8958	7021.7916	0.5642	0.5642
GTRIG	45	-3466.9063	7023.8126	0.2054	0.7696
HKYG	40	-3472.1095	7024.2189	0.1676	0.9372
HKYIG	41	-3472.1097	7026.2195	0.0617	0.9989
GTRI	44	-3473.2482	7034.4963	0.0010	0.9999
HKYI	40	-3479.2442	7038.4883	0.0001	1.0000
K2PG	37	-3506.9957	7087.9915	0.0000	1.0000
K2PIG	38	-3506.9957	7089.9913	0.0000	1.0000
SYMG	41	-3505.5344	7093.0688	0.0000	1.0000
SYMIG	42	-3505.5345	7095.0690	0.0000	1.0000
K2PI	37	-3515.5786	7105.1572	0.0000	1.0000
SYMI	41	-3514.1518	7110.3035	0.0000	1.0000
HKY	39	-3529.1859	7136.3718	0.0000	1.0000
GTR	43	-3525.5507	7137.1015	0.0000	1.0000
K2P	36	-3561.8763	7195.7526	0.0000	1.0000
SYM	40	-3559.0538	7198.1076	0.0000	1.0000
F81G	39	-3570.1809	7218.3619	0.0000	1.0000
F81IG	40	-3570.1810	7220.3620	0.0000	1.0000
F81I	39	-3576.3947	7230.7893	0.0000	1.0000
JC69G	36	-3595.8174	7263.6348	0.0000	1.0000
JC69IG	37	-3595.8174	7265.6349	0.0000	1.0000
JC69I	36	-3602.9890	7277.9780	0.0000	1.0000
F81	38	-3621.5738	7319.1476	0.0000	1.0000
JC69	35	-3646.1443	7362.2887	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3472.1095	7208.8615	0.9637	0.9637
HKYIG	41	-3472.1097	7215.4782	0.0352	0.9989
HKYI	40	-3479.2442	7223.1309	0.0008	0.9997
GTRG	44	-3466.8958	7224.8984	0.0003	1.0000
GTRIG	45	-3466.9063	7231.5356	0.0000	1.0000
GTRI	44	-3473.2482	7237.6032	0.0000	1.0000
K2PG	37	-3506.9957	7258.7859	0.0000	1.0000
K2PIG	38	-3506.9957	7265.4018	0.0000	1.0000
K2PI	37	-3515.5786	7275.9516	0.0000	1.0000
SYMG	41	-3505.5344	7282.3275	0.0000	1.0000
SYMIG	42	-3505.5345	7288.9437	0.0000	1.0000
SYMI	41	-3514.1518	7299.5622	0.0000	1.0000
HKY	39	-3529.1859	7316.3983	0.0000	1.0000
GTR	43	-3525.5507	7335.5923	0.0000	1.0000
K2P	36	-3561.8763	7361.9309	0.0000	1.0000
SYM	40	-3559.0538	7382.7502	0.0000	1.0000
F81G	39	-3570.1809	7398.3884	0.0000	1.0000
F81IG	40	-3570.1810	7405.0046	0.0000	1.0000
F81I	39	-3576.3947	7410.8159	0.0000	1.0000
JC69G	36	-3595.8174	7429.8131	0.0000	1.0000
JC69IG	37	-3595.8174	7436.4293	0.0000	1.0000
JC69I	36	-3602.9890	7444.1563	0.0000	1.0000
F81	38	-3621.5738	7494.5581	0.0000	1.0000
JC69	35	-3646.1443	7523.8510	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip = 1 - 747;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_4680.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

