
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:56 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/chr7_10431.phylip" (19 taxa, 938 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: HKYIG
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
HKYIG	41	-2599.1858	5284.2154	0.3943	0.3943
GTRIG	45	-2594.8405	5284.3222	0.3738	0.7681
HKYG	40	-2601.7716	5287.1998	0.0887	0.8568
GTRG	44	-2597.4391	5287.3126	0.0838	0.9406
HKYI	40	-2602.7297	5289.1160	0.0340	0.9746
GTRI	44	-2598.6341	5289.7027	0.0254	1.0000
K2PIG	38	-2636.8947	5353.0864	0.0000	1.0000
K2PG	37	-2639.3113	5355.7470	0.0000	1.0000
K2PI	37	-2640.0764	5357.2773	0.0000	1.0000
SYMIG	42	-2636.1632	5360.3622	0.0000	1.0000
SYMG	41	-2638.5199	5362.8836	0.0000	1.0000
SYMI	41	-2639.3265	5364.4967	0.0000	1.0000
F81IG	40	-2672.1523	5427.9613	0.0000	1.0000
F81G	39	-2673.9798	5429.4340	0.0000	1.0000
F81I	39	-2674.8398	5431.1540	0.0000	1.0000
GTR	43	-2672.4337	5435.1001	0.0000	1.0000
HKY	39	-2678.0062	5437.4869	0.0000	1.0000
JC69IG	37	-2709.4022	5495.9289	0.0000	1.0000
JC69G	36	-2711.4318	5497.8203	0.0000	1.0000
JC69I	36	-2712.3187	5499.5940	0.0000	1.0000
K2P	36	-2715.9200	5506.7967	0.0000	1.0000
SYM	40	-2714.4207	5512.4980	0.0000	1.0000
F81	38	-2747.0630	5573.4231	0.0000	1.0000
JC69	35	-2785.6222	5644.0382	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2594.8405	5279.6810	0.4604	0.4604
HKYIG	41	-2599.1858	5280.3717	0.3260	0.7864
GTRG	44	-2597.4391	5282.8781	0.0931	0.8795
HKYG	40	-2601.7716	5283.5431	0.0668	0.9462
GTRI	44	-2598.6341	5285.2682	0.0282	0.9744
HKYI	40	-2602.7297	5285.4594	0.0256	1.0000
K2PIG	38	-2636.8947	5349.7894	0.0000	1.0000
K2PG	37	-2639.3113	5352.6226	0.0000	1.0000
K2PI	37	-2640.0764	5354.1529	0.0000	1.0000
SYMIG	42	-2636.1632	5356.3264	0.0000	1.0000
SYMG	41	-2638.5199	5359.0399	0.0000	1.0000
SYMI	41	-2639.3265	5360.6529	0.0000	1.0000
F81IG	40	-2672.1523	5424.3047	0.0000	1.0000
F81G	39	-2673.9798	5425.9597	0.0000	1.0000
F81I	39	-2674.8398	5427.6796	0.0000	1.0000
GTR	43	-2672.4337	5430.8674	0.0000	1.0000
HKY	39	-2678.0062	5434.0125	0.0000	1.0000
JC69IG	37	-2709.4022	5492.8044	0.0000	1.0000
JC69G	36	-2711.4318	5494.8635	0.0000	1.0000
JC69I	36	-2712.3187	5496.6373	0.0000	1.0000
K2P	36	-2715.9200	5503.8400	0.0000	1.0000
SYM	40	-2714.4207	5508.8414	0.0000	1.0000
F81	38	-2747.0630	5570.1261	0.0000	1.0000
JC69	35	-2785.6222	5641.2444	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2601.7716	5477.2931	0.5503	0.5503
HKYIG	41	-2599.1858	5478.9654	0.2385	0.7888
HKYI	40	-2602.7297	5479.2094	0.2111	0.9999
GTRG	44	-2597.4391	5496.0031	0.0000	1.0000
GTRIG	45	-2594.8405	5497.6497	0.0000	1.0000
GTRI	44	-2598.6341	5498.3932	0.0000	1.0000
K2PG	37	-2639.3113	5531.8413	0.0000	1.0000
K2PI	37	-2640.0764	5533.3716	0.0000	1.0000
K2PIG	38	-2636.8947	5533.8519	0.0000	1.0000
SYMG	41	-2638.5199	5557.6336	0.0000	1.0000
SYMI	41	-2639.3265	5559.2466	0.0000	1.0000
SYMIG	42	-2636.1632	5559.7639	0.0000	1.0000
F81G	39	-2673.9798	5614.8659	0.0000	1.0000
F81I	39	-2674.8398	5616.5858	0.0000	1.0000
F81IG	40	-2672.1523	5618.0547	0.0000	1.0000
HKY	39	-2678.0062	5622.9187	0.0000	1.0000
GTR	43	-2672.4337	5639.1487	0.0000	1.0000
JC69G	36	-2711.4318	5669.2385	0.0000	1.0000
JC69I	36	-2712.3187	5671.0123	0.0000	1.0000
JC69IG	37	-2709.4022	5672.0232	0.0000	1.0000
K2P	36	-2715.9200	5678.2150	0.0000	1.0000
SYM	40	-2714.4207	5702.5914	0.0000	1.0000
F81	38	-2747.0630	5754.1886	0.0000	1.0000
JC69	35	-2785.6222	5810.7756	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10431.phylip = 1 - 938;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10431.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10431.phylip = 1 - 938;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10431.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr7_10431.phylip = 1 - 938;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10431.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

