
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:38 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_10201.phylip" (19 taxa, 884 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	-2687.3782	5460.8467	0.3821	0.3821
GTRIG	45	-2683.1471	5461.2345	0.3148	0.6969
GTRG	44	-2684.7943	5462.3085	0.1840	0.8809
HKYG	40	-2689.6896	5463.2701	0.1138	0.9946
GTRI	44	-2688.7968	5470.3135	0.0034	0.9980
HKYI	40	-2693.7239	5471.3386	0.0020	1.0000
F81IG	40	-2720.8972	5525.6853	0.0000	1.0000
F81G	39	-2722.6841	5527.0649	0.0000	1.0000
F81I	39	-2725.9705	5533.6377	0.0000	1.0000
K2PIG	38	-2734.3960	5548.2997	0.0000	1.0000
K2PG	37	-2736.2619	5549.8476	0.0000	1.0000
SYMIG	42	-2732.4509	5553.1967	0.0000	1.0000
SYMG	41	-2734.3508	5554.7919	0.0000	1.0000
K2PI	37	-2739.3123	5555.9485	0.0000	1.0000
SYMI	41	-2741.2200	5568.5302	0.0000	1.0000
GTR	43	-2743.5433	5577.5913	0.0000	1.0000
HKY	39	-2750.3162	5582.3292	0.0000	1.0000
JC69G	36	-2768.5768	5612.2988	0.0000	1.0000
JC69IG	37	-2769.6193	5616.5626	0.0000	1.0000
JC69I	36	-2774.4549	5624.0549	0.0000	1.0000
F81	38	-2780.8614	5641.2305	0.0000	1.0000
K2P	36	-2794.7687	5664.6826	0.0000	1.0000
SYM	40	-2793.1106	5670.1121	0.0000	1.0000
JC69	35	-2826.5746	5726.1208	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2683.1471	5456.2941	0.3930	0.3930
HKYIG	41	-2687.3782	5456.7564	0.3119	0.7050
GTRG	44	-2684.7943	5457.5886	0.2058	0.9107
HKYG	40	-2689.6896	5459.3792	0.0840	0.9948
GTRI	44	-2688.7968	5465.5936	0.0038	0.9985
HKYI	40	-2693.7239	5467.4478	0.0015	1.0000
F81IG	40	-2720.8972	5521.7945	0.0000	1.0000
F81G	39	-2722.6841	5523.3682	0.0000	1.0000
F81I	39	-2725.9705	5529.9411	0.0000	1.0000
K2PIG	38	-2734.3960	5544.7920	0.0000	1.0000
K2PG	37	-2736.2619	5546.5237	0.0000	1.0000
SYMIG	42	-2732.4509	5548.9018	0.0000	1.0000
SYMG	41	-2734.3508	5550.7016	0.0000	1.0000
K2PI	37	-2739.3123	5552.6247	0.0000	1.0000
SYMI	41	-2741.2200	5564.4399	0.0000	1.0000
GTR	43	-2743.5433	5573.0865	0.0000	1.0000
HKY	39	-2750.3162	5578.6325	0.0000	1.0000
JC69G	36	-2768.5768	5609.1536	0.0000	1.0000
JC69IG	37	-2769.6193	5613.2387	0.0000	1.0000
JC69I	36	-2774.4549	5620.9097	0.0000	1.0000
F81	38	-2780.8614	5637.7228	0.0000	1.0000
K2P	36	-2794.7687	5661.5374	0.0000	1.0000
SYM	40	-2793.1106	5666.2213	0.0000	1.0000
JC69	35	-2826.5746	5723.1491	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2689.6896	5650.7575	0.7368	0.7368
HKYIG	41	-2687.3782	5652.9191	0.2500	0.9868
HKYI	40	-2693.7239	5658.8261	0.0130	0.9998
GTRG	44	-2684.7943	5668.1047	0.0001	1.0000
GTRIG	45	-2683.1471	5671.5947	0.0000	1.0000
GTRI	44	-2688.7968	5676.1097	0.0000	1.0000
F81G	39	-2722.6841	5709.9620	0.0000	1.0000
F81IG	40	-2720.8972	5713.1728	0.0000	1.0000
F81I	39	-2725.9705	5716.5349	0.0000	1.0000
K2PG	37	-2736.2619	5723.5486	0.0000	1.0000
K2PIG	38	-2734.3960	5726.6014	0.0000	1.0000
K2PI	37	-2739.3123	5729.6496	0.0000	1.0000
SYMG	41	-2734.3508	5746.8644	0.0000	1.0000
SYMIG	42	-2732.4509	5749.8490	0.0000	1.0000
SYMI	41	-2741.2200	5760.6027	0.0000	1.0000
HKY	39	-2750.3162	5765.2263	0.0000	1.0000
GTR	43	-2743.5433	5778.8182	0.0000	1.0000
JC69G	36	-2768.5768	5781.3940	0.0000	1.0000
JC69IG	37	-2769.6193	5790.2636	0.0000	1.0000
JC69I	36	-2774.4549	5793.1502	0.0000	1.0000
F81	38	-2780.8614	5819.5321	0.0000	1.0000
K2P	36	-2794.7687	5833.7779	0.0000	1.0000
SYM	40	-2793.1106	5857.5996	0.0000	1.0000
JC69	35	-2826.5746	5890.6051	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/chr5_10201.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10201.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/chr5_10201.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10201.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/chr5_10201.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10201.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

