
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:07 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_14374.phylip" (19 taxa, 394 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	-1229.6334	2558.6134	0.5816	0.5816
GTRIG	45	-1229.3892	2560.6750	0.2075	0.7891
GTRI	44	-1230.8121	2560.9709	0.1789	0.9680
HKYG	40	-1238.2473	2565.7865	0.0161	0.9841
HKYI	40	-1238.7475	2566.7868	0.0098	0.9939
HKYIG	41	-1237.9672	2567.7185	0.0061	1.0000
K2PG	37	-1253.4172	2588.7333	0.0000	1.0000
K2PI	37	-1254.6961	2591.2912	0.0000	1.0000
SYMG	41	-1249.9940	2591.7721	0.0000	1.0000
K2PIG	38	-1254.0983	2592.5459	0.0000	1.0000
SYMIG	42	-1250.3359	2594.9624	0.0000	1.0000
GTR	43	-1249.4308	2595.6730	0.0000	1.0000
SYMI	41	-1252.3830	2596.5502	0.0000	1.0000
HKY	39	-1256.6536	2600.1208	0.0000	1.0000
K2P	36	-1271.3530	2622.1683	0.0000	1.0000
F81G	39	-1267.8472	2622.5079	0.0000	1.0000
SYM	40	-1268.4880	2626.2679	0.0000	1.0000
F81I	39	-1269.9739	2626.7613	0.0000	1.0000
F81IG	40	-1269.3412	2627.9742	0.0000	1.0000
JC69G	36	-1281.6958	2642.8538	0.0000	1.0000
JC69IG	37	-1281.5326	2644.9642	0.0000	1.0000
JC69I	36	-1284.5097	2648.4816	0.0000	1.0000
F81	38	-1285.4817	2655.3127	0.0000	1.0000
JC69	35	-1299.1279	2675.2949	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1229.6334	2547.2667	0.5562	0.5562
GTRIG	45	-1229.3892	2548.7784	0.2612	0.8173
GTRI	44	-1230.8121	2549.6242	0.1711	0.9885
HKYG	40	-1238.2473	2556.4947	0.0055	0.9940
HKYI	40	-1238.7475	2557.4951	0.0033	0.9973
HKYIG	41	-1237.9672	2557.9344	0.0027	1.0000
K2PG	37	-1253.4172	2580.8345	0.0000	1.0000
SYMG	41	-1249.9940	2581.9880	0.0000	1.0000
K2PI	37	-1254.6961	2583.3923	0.0000	1.0000
K2PIG	38	-1254.0983	2584.1966	0.0000	1.0000
SYMIG	42	-1250.3359	2584.6718	0.0000	1.0000
GTR	43	-1249.4308	2584.8615	0.0000	1.0000
SYMI	41	-1252.3830	2586.7661	0.0000	1.0000
HKY	39	-1256.6536	2591.3072	0.0000	1.0000
F81G	39	-1267.8472	2613.6943	0.0000	1.0000
K2P	36	-1271.3530	2614.7061	0.0000	1.0000
SYM	40	-1268.4880	2616.9761	0.0000	1.0000
F81I	39	-1269.9739	2617.9477	0.0000	1.0000
F81IG	40	-1269.3412	2618.6824	0.0000	1.0000
JC69G	36	-1281.6958	2635.3916	0.0000	1.0000
JC69IG	37	-1281.5326	2637.0653	0.0000	1.0000
JC69I	36	-1284.5097	2641.0194	0.0000	1.0000
F81	38	-1285.4817	2646.9634	0.0000	1.0000
JC69	35	-1299.1279	2668.2558	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1238.2473	2715.5487	0.5799	0.5799
HKYI	40	-1238.7475	2716.5491	0.3517	0.9316
HKYIG	41	-1237.9672	2720.9648	0.0387	0.9702
GTRG	44	-1229.6334	2722.2262	0.0206	0.9908
GTRI	44	-1230.8121	2724.5836	0.0063	0.9972
GTRIG	45	-1229.3892	2727.7142	0.0013	0.9985
K2PG	37	-1253.4172	2727.9594	0.0012	0.9996
K2PI	37	-1254.6961	2730.5173	0.0003	1.0000
K2PIG	38	-1254.0983	2735.2979	0.0000	1.0000
SYMG	41	-1249.9940	2745.0184	0.0000	1.0000
HKY	39	-1256.6536	2746.3849	0.0000	1.0000
SYMI	41	-1252.3830	2749.7965	0.0000	1.0000
SYMIG	42	-1250.3359	2751.6786	0.0000	1.0000
GTR	43	-1249.4308	2755.8446	0.0000	1.0000
K2P	36	-1271.3530	2757.8547	0.0000	1.0000
F81G	39	-1267.8472	2768.7720	0.0000	1.0000
F81I	39	-1269.9739	2773.0254	0.0000	1.0000
SYM	40	-1268.4880	2776.0301	0.0000	1.0000
F81IG	40	-1269.3412	2777.7365	0.0000	1.0000
JC69G	36	-1281.6958	2778.5402	0.0000	1.0000
JC69I	36	-1284.5097	2784.1681	0.0000	1.0000
JC69IG	37	-1281.5326	2784.1903	0.0000	1.0000
F81	38	-1285.4817	2798.0647	0.0000	1.0000
JC69	35	-1299.1279	2807.4280	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_14374.phylip = 1 - 394;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14374.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_14374.phylip = 1 - 394;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14374.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_14374.phylip = 1 - 394;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14374.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

