
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:10 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/chrZ_6686.phylip" (19 taxa, 765 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	-2570.0253	5233.5507	0.7295	0.7295
GTRIG	45	-2569.9857	5235.7295	0.2454	0.9749
HKYG	40	-2578.2198	5240.9700	0.0179	0.9928
HKYIG	41	-2578.1459	5243.0554	0.0063	0.9991
GTRI	44	-2576.7693	5247.0386	0.0009	0.9999
HKYI	40	-2583.8541	5252.2385	0.0001	1.0000
SYMG	41	-2599.8597	5286.4828	0.0000	1.0000
K2PG	37	-2604.7943	5287.4565	0.0000	1.0000
SYMIG	42	-2599.8301	5288.6631	0.0000	1.0000
K2PIG	38	-2604.7479	5289.5783	0.0000	1.0000
GTR	43	-2602.1591	5295.5665	0.0000	1.0000
SYMI	41	-2605.8350	5298.4335	0.0000	1.0000
K2PI	37	-2610.4018	5298.6716	0.0000	1.0000
HKY	39	-2610.4187	5303.1408	0.0000	1.0000
SYM	40	-2628.0269	5340.5843	0.0000	1.0000
K2P	36	-2633.6658	5342.9909	0.0000	1.0000
F81G	39	-2662.7059	5407.7152	0.0000	1.0000
F81IG	40	-2662.6957	5409.9217	0.0000	1.0000
F81I	39	-2667.7486	5417.8006	0.0000	1.0000
JC69G	36	-2683.9393	5443.5379	0.0000	1.0000
JC69IG	37	-2683.9327	5445.7333	0.0000	1.0000
JC69I	36	-2688.6989	5453.0572	0.0000	1.0000
F81	38	-2689.3374	5458.7575	0.0000	1.0000
JC69	35	-2709.3858	5492.2283	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2570.0253	5228.0507	0.7117	0.7117
GTRIG	45	-2569.9857	5229.9715	0.2724	0.9841
HKYG	40	-2578.2198	5236.4396	0.0107	0.9949
HKYIG	41	-2578.1459	5238.2919	0.0043	0.9991
GTRI	44	-2576.7693	5241.5386	0.0008	1.0000
HKYI	40	-2583.8541	5247.7082	0.0000	1.0000
SYMG	41	-2599.8597	5281.7193	0.0000	1.0000
K2PG	37	-2604.7943	5283.5886	0.0000	1.0000
SYMIG	42	-2599.8301	5283.6603	0.0000	1.0000
K2PIG	38	-2604.7479	5285.4957	0.0000	1.0000
GTR	43	-2602.1591	5290.3182	0.0000	1.0000
SYMI	41	-2605.8350	5293.6700	0.0000	1.0000
K2PI	37	-2610.4018	5294.8037	0.0000	1.0000
HKY	39	-2610.4187	5298.8373	0.0000	1.0000
SYM	40	-2628.0269	5336.0539	0.0000	1.0000
K2P	36	-2633.6658	5339.3316	0.0000	1.0000
F81G	39	-2662.7059	5403.4117	0.0000	1.0000
F81IG	40	-2662.6957	5405.3913	0.0000	1.0000
F81I	39	-2667.7486	5413.4972	0.0000	1.0000
JC69G	36	-2683.9393	5439.8786	0.0000	1.0000
JC69IG	37	-2683.9327	5441.8653	0.0000	1.0000
JC69I	36	-2688.6989	5449.3979	0.0000	1.0000
F81	38	-2689.3374	5454.6749	0.0000	1.0000
JC69	35	-2709.3858	5488.7715	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2578.2198	5422.0346	0.9534	0.9534
HKYIG	41	-2578.1459	5428.5268	0.0371	0.9905
GTRG	44	-2570.0253	5432.2052	0.0059	0.9964
HKYI	40	-2583.8541	5433.3032	0.0034	0.9998
GTRIG	45	-2569.9857	5438.7659	0.0002	1.0000
GTRI	44	-2576.7693	5445.6931	0.0000	1.0000
K2PG	37	-2604.7943	5455.2640	0.0000	1.0000
K2PIG	38	-2604.7479	5461.8110	0.0000	1.0000
K2PI	37	-2610.4018	5466.4791	0.0000	1.0000
SYMG	41	-2599.8597	5471.9542	0.0000	1.0000
SYMIG	42	-2599.8301	5478.5351	0.0000	1.0000
HKY	39	-2610.4187	5479.7925	0.0000	1.0000
SYMI	41	-2605.8350	5483.9049	0.0000	1.0000
GTR	43	-2602.1591	5489.8329	0.0000	1.0000
K2P	36	-2633.6658	5506.3671	0.0000	1.0000
SYM	40	-2628.0269	5521.6489	0.0000	1.0000
F81G	39	-2662.7059	5584.3669	0.0000	1.0000
F81IG	40	-2662.6957	5590.9863	0.0000	1.0000
F81I	39	-2667.7486	5594.4523	0.0000	1.0000
JC69G	36	-2683.9393	5606.9141	0.0000	1.0000
JC69IG	37	-2683.9327	5613.5407	0.0000	1.0000
JC69I	36	-2688.6989	5616.4334	0.0000	1.0000
F81	38	-2689.3374	5630.9902	0.0000	1.0000
JC69	35	-2709.3858	5651.1672	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/chrZ_6686.phylip = 1 - 765;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6686.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/chrZ_6686.phylip = 1 - 765;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6686.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/chrZ_6686.phylip = 1 - 765;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6686.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

