
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:53 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/chr2_21265.phylip" (19 taxa, 482 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	-1673.5565	3444.1747	0.4717	0.4717
GTRI	44	-1674.3186	3445.6989	0.2201	0.6918
GTRIG	45	-1673.5564	3446.6081	0.1397	0.8315
HKYG	40	-1679.9242	3447.2861	0.0995	0.9311
HKYI	40	-1680.8724	3449.1825	0.0386	0.9696
HKYIG	41	-1679.9162	3449.6597	0.0304	1.0000
K2PG	37	-1702.6904	3485.7142	0.0000	1.0000
K2PIG	38	-1702.5796	3487.8500	0.0000	1.0000
K2PI	37	-1703.9818	3488.2969	0.0000	1.0000
SYMG	41	-1701.4591	3492.7454	0.0000	1.0000
SYMI	41	-1702.8250	3495.4773	0.0000	1.0000
SYMIG	42	-1702.5813	3497.3903	0.0000	1.0000
GTR	43	-1708.8277	3512.2947	0.0000	1.0000
HKY	39	-1717.2925	3519.6438	0.0000	1.0000
F81G	39	-1724.1471	3533.3530	0.0000	1.0000
F81IG	40	-1723.9926	3535.4228	0.0000	1.0000
F81I	39	-1725.5339	3536.1266	0.0000	1.0000
JC69G	36	-1743.5809	3565.1483	0.0000	1.0000
K2P	36	-1743.7321	3565.4508	0.0000	1.0000
JC69IG	37	-1743.3080	3566.9494	0.0000	1.0000
SYM	40	-1739.8330	3567.1037	0.0000	1.0000
JC69I	36	-1745.2140	3568.4145	0.0000	1.0000
F81	38	-1764.7333	3612.1573	0.0000	1.0000
JC69	35	-1785.9327	3647.5155	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1673.5565	3435.1130	0.5002	0.5002
GTRI	44	-1674.3186	3436.6371	0.2334	0.7336
GTRIG	45	-1673.5564	3437.1127	0.1840	0.9176
HKYG	40	-1679.9242	3439.8484	0.0469	0.9645
HKYI	40	-1680.8724	3441.7448	0.0182	0.9826
HKYIG	41	-1679.9162	3441.8324	0.0174	1.0000
K2PG	37	-1702.6904	3479.3809	0.0000	1.0000
K2PIG	38	-1702.5796	3481.1593	0.0000	1.0000
K2PI	37	-1703.9818	3481.9636	0.0000	1.0000
SYMG	41	-1701.4591	3484.9182	0.0000	1.0000
SYMI	41	-1702.8250	3487.6500	0.0000	1.0000
SYMIG	42	-1702.5813	3489.1625	0.0000	1.0000
GTR	43	-1708.8277	3503.6555	0.0000	1.0000
HKY	39	-1717.2925	3512.5850	0.0000	1.0000
F81G	39	-1724.1471	3526.2942	0.0000	1.0000
F81IG	40	-1723.9926	3527.9851	0.0000	1.0000
F81I	39	-1725.5339	3529.0678	0.0000	1.0000
JC69G	36	-1743.5809	3559.1618	0.0000	1.0000
K2P	36	-1743.7321	3559.4643	0.0000	1.0000
SYM	40	-1739.8330	3559.6661	0.0000	1.0000
JC69IG	37	-1743.3080	3560.6161	0.0000	1.0000
JC69I	36	-1745.2140	3562.4280	0.0000	1.0000
F81	38	-1764.7333	3605.4665	0.0000	1.0000
JC69	35	-1785.9327	3641.8653	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1679.9242	3606.9662	0.6958	0.6958
HKYI	40	-1680.8724	3608.8626	0.2696	0.9654
HKYIG	41	-1679.9162	3613.1281	0.0319	0.9974
GTRG	44	-1673.5565	3618.9425	0.0017	0.9991
GTRI	44	-1674.3186	3620.4667	0.0008	0.9999
GTRIG	45	-1673.5564	3625.1202	0.0001	1.0000
K2PG	37	-1702.6904	3633.9648	0.0000	1.0000
K2PI	37	-1703.9818	3636.5475	0.0000	1.0000
K2PIG	38	-1702.5796	3639.9212	0.0000	1.0000
SYMG	41	-1701.4591	3656.2139	0.0000	1.0000
SYMI	41	-1702.8250	3658.9457	0.0000	1.0000
SYMIG	42	-1702.5813	3664.6362	0.0000	1.0000
HKY	39	-1717.2925	3675.5248	0.0000	1.0000
GTR	43	-1708.8277	3683.3071	0.0000	1.0000
F81G	39	-1724.1471	3689.2340	0.0000	1.0000
F81I	39	-1725.5339	3692.0076	0.0000	1.0000
F81IG	40	-1723.9926	3695.1029	0.0000	1.0000
JC69G	36	-1743.5809	3709.5678	0.0000	1.0000
K2P	36	-1743.7321	3709.8702	0.0000	1.0000
JC69I	36	-1745.2140	3712.8340	0.0000	1.0000
JC69IG	37	-1743.3080	3715.2000	0.0000	1.0000
SYM	40	-1739.8330	3726.7839	0.0000	1.0000
F81	38	-1764.7333	3764.2284	0.0000	1.0000
JC69	35	-1785.9327	3788.0934	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/chr2_21265.phylip = 1 - 482;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21265.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/chr2_21265.phylip = 1 - 482;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21265.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/chr2_21265.phylip = 1 - 482;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21265.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

