
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:43 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/chr5_14864.phylip" (19 taxa, 664 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	-2618.9482	5332.2938	0.6525	0.6525
GTRIG	45	-2618.8065	5334.3120	0.2379	0.8903
HKYG	40	-2626.0441	5337.3530	0.0520	0.9423
GTRI	44	-2621.8890	5338.1754	0.0345	0.9768
HKYIG	41	-2625.8736	5339.2843	0.0198	0.9966
HKYI	40	-2628.7683	5342.8014	0.0034	1.0000
K2PG	37	-2638.5419	5355.5758	0.0000	1.0000
SYMG	41	-2634.9614	5357.4597	0.0000	1.0000
K2PIG	38	-2638.3784	5357.4993	0.0000	1.0000
SYMIG	42	-2634.8609	5359.5383	0.0000	1.0000
K2PI	37	-2641.2970	5361.0859	0.0000	1.0000
SYMI	41	-2637.8610	5363.2589	0.0000	1.0000
GTR	43	-2652.0897	5396.2826	0.0000	1.0000
HKY	39	-2659.5149	5402.0299	0.0000	1.0000
K2P	36	-2672.7665	5421.7819	0.0000	1.0000
SYM	40	-2668.4963	5422.2574	0.0000	1.0000
F81G	39	-2679.6312	5442.2625	0.0000	1.0000
F81IG	40	-2679.5166	5444.2981	0.0000	1.0000
F81I	39	-2682.3618	5447.7236	0.0000	1.0000
JC69G	36	-2692.0415	5460.3318	0.0000	1.0000
JC69IG	37	-2691.9242	5462.3404	0.0000	1.0000
JC69I	36	-2694.8658	5465.9805	0.0000	1.0000
F81	38	-2712.3059	5505.3542	0.0000	1.0000
JC69	35	-2725.3285	5524.6697	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2618.9482	5325.8964	0.6474	0.6474
GTRIG	45	-2618.8065	5327.6130	0.2744	0.9218
GTRI	44	-2621.8890	5331.7780	0.0342	0.9560
HKYG	40	-2626.0441	5332.0882	0.0293	0.9853
HKYIG	41	-2625.8736	5333.7473	0.0128	0.9981
HKYI	40	-2628.7683	5337.5366	0.0019	1.0000
K2PG	37	-2638.5419	5351.0837	0.0000	1.0000
SYMG	41	-2634.9614	5351.9228	0.0000	1.0000
K2PIG	38	-2638.3784	5352.7569	0.0000	1.0000
SYMIG	42	-2634.8609	5353.7218	0.0000	1.0000
K2PI	37	-2641.2970	5356.5939	0.0000	1.0000
SYMI	41	-2637.8610	5357.7219	0.0000	1.0000
GTR	43	-2652.0897	5390.1793	0.0000	1.0000
HKY	39	-2659.5149	5397.0299	0.0000	1.0000
SYM	40	-2668.4963	5416.9925	0.0000	1.0000
K2P	36	-2672.7665	5417.5331	0.0000	1.0000
F81G	39	-2679.6312	5437.2625	0.0000	1.0000
F81IG	40	-2679.5166	5439.0332	0.0000	1.0000
F81I	39	-2682.3618	5442.7236	0.0000	1.0000
JC69G	36	-2692.0415	5456.0830	0.0000	1.0000
JC69IG	37	-2691.9242	5457.8484	0.0000	1.0000
JC69I	36	-2694.8658	5461.7317	0.0000	1.0000
F81	38	-2712.3059	5500.6118	0.0000	1.0000
JC69	35	-2725.3285	5520.6570	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2626.0441	5512.0195	0.8435	0.8435
HKYI	40	-2628.7683	5517.4678	0.0553	0.8988
K2PG	37	-2638.5419	5517.5202	0.0539	0.9528
HKYIG	41	-2625.8736	5518.1769	0.0388	0.9916
K2PI	37	-2641.2970	5523.0304	0.0034	0.9950
K2PIG	38	-2638.3784	5523.6916	0.0025	0.9975
GTRG	44	-2618.9482	5523.8208	0.0023	0.9998
GTRI	44	-2621.8890	5529.7024	0.0001	0.9999
GTRIG	45	-2618.8065	5530.0357	0.0001	1.0000
SYMG	41	-2634.9614	5536.3523	0.0000	1.0000
SYMI	41	-2637.8610	5542.1515	0.0000	1.0000
SYMIG	42	-2634.8609	5542.6497	0.0000	1.0000
HKY	39	-2659.5149	5572.4629	0.0000	1.0000
K2P	36	-2672.7665	5579.4712	0.0000	1.0000
GTR	43	-2652.0897	5583.6055	0.0000	1.0000
SYM	40	-2668.4963	5596.9238	0.0000	1.0000
F81G	39	-2679.6312	5612.6955	0.0000	1.0000
JC69G	36	-2692.0415	5618.0212	0.0000	1.0000
F81I	39	-2682.3618	5618.1566	0.0000	1.0000
F81IG	40	-2679.5166	5618.9645	0.0000	1.0000
JC69I	36	-2694.8658	5623.6698	0.0000	1.0000
JC69IG	37	-2691.9242	5624.2849	0.0000	1.0000
F81	38	-2712.3059	5671.5465	0.0000	1.0000
JC69	35	-2725.3285	5678.0969	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/chr5_14864.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14864.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/chr5_14864.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14864.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/chr5_14864.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14864.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

