
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:49 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_18926.phylip" (19 taxa, 526 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	-2445.0852	4986.4033	0.7645	0.7645
GTRIG	45	-2445.0852	4988.7954	0.2312	0.9957
GTRI	44	-2450.8131	4997.8591	0.0025	0.9982
HKYG	40	-2456.1284	4999.0196	0.0014	0.9996
HKYIG	41	-2456.1284	5001.3724	0.0004	1.0000
HKYI	40	-2461.9018	5010.5665	0.0000	1.0000
K2PG	37	-2479.9786	5039.7194	0.0000	1.0000
K2PIG	38	-2479.9785	5042.0433	0.0000	1.0000
SYMG	41	-2477.9468	5045.0093	0.0000	1.0000
SYMIG	42	-2477.9467	5047.3717	0.0000	1.0000
K2PI	37	-2486.8954	5053.5531	0.0000	1.0000
SYMI	41	-2484.3943	5057.9042	0.0000	1.0000
GTR	43	-2498.2090	5090.2687	0.0000	1.0000
HKY	39	-2507.9013	5100.2224	0.0000	1.0000
K2P	36	-2533.3685	5144.1849	0.0000	1.0000
SYM	40	-2530.3922	5147.5472	0.0000	1.0000
F81G	39	-2548.8452	5182.1101	0.0000	1.0000
F81IG	40	-2548.8452	5184.4534	0.0000	1.0000
F81I	39	-2554.7038	5193.8274	0.0000	1.0000
JC69G	36	-2563.5004	5204.4487	0.0000	1.0000
JC69IG	37	-2563.5005	5206.7632	0.0000	1.0000
JC69I	36	-2569.8858	5217.2194	0.0000	1.0000
F81	38	-2598.4163	5278.9187	0.0000	1.0000
JC69	35	-2614.1159	5303.3747	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2445.0852	4978.1705	0.7287	0.7287
GTRIG	45	-2445.0852	4980.1704	0.2681	0.9968
GTRI	44	-2450.8131	4989.6262	0.0024	0.9991
HKYG	40	-2456.1284	4992.2568	0.0006	0.9998
HKYIG	41	-2456.1284	4994.2567	0.0002	1.0000
HKYI	40	-2461.9018	5003.8036	0.0000	1.0000
K2PG	37	-2479.9786	5033.9571	0.0000	1.0000
K2PIG	38	-2479.9785	5035.9571	0.0000	1.0000
SYMG	41	-2477.9468	5037.8936	0.0000	1.0000
SYMIG	42	-2477.9467	5039.8934	0.0000	1.0000
K2PI	37	-2486.8954	5047.7908	0.0000	1.0000
SYMI	41	-2484.3943	5050.7885	0.0000	1.0000
GTR	43	-2498.2090	5082.4181	0.0000	1.0000
HKY	39	-2507.9013	5093.8026	0.0000	1.0000
K2P	36	-2533.3685	5138.7370	0.0000	1.0000
SYM	40	-2530.3922	5140.7843	0.0000	1.0000
F81G	39	-2548.8452	5175.6903	0.0000	1.0000
F81IG	40	-2548.8452	5177.6905	0.0000	1.0000
F81I	39	-2554.7038	5187.4077	0.0000	1.0000
JC69G	36	-2563.5004	5199.0008	0.0000	1.0000
JC69IG	37	-2563.5005	5201.0009	0.0000	1.0000
JC69I	36	-2569.8858	5211.7716	0.0000	1.0000
F81	38	-2598.4163	5272.8325	0.0000	1.0000
JC69	35	-2614.1159	5298.2319	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2456.1284	5162.8688	0.7793	0.7793
GTRG	44	-2445.0852	5165.8437	0.1761	0.9553
HKYIG	41	-2456.1284	5169.1341	0.0340	0.9893
GTRIG	45	-2445.0852	5172.1090	0.0077	0.9970
HKYI	40	-2461.9018	5174.4156	0.0024	0.9994
GTRI	44	-2450.8131	5177.2995	0.0006	1.0000
K2PG	37	-2479.9786	5191.7733	0.0000	1.0000
K2PIG	38	-2479.9785	5198.0385	0.0000	1.0000
K2PI	37	-2486.8954	5205.6069	0.0000	1.0000
SYMG	41	-2477.9468	5212.7709	0.0000	1.0000
SYMIG	42	-2477.9467	5219.0361	0.0000	1.0000
SYMI	41	-2484.3943	5225.6659	0.0000	1.0000
HKY	39	-2507.9013	5260.1494	0.0000	1.0000
GTR	43	-2498.2090	5265.8260	0.0000	1.0000
K2P	36	-2533.3685	5292.2879	0.0000	1.0000
SYM	40	-2530.3922	5311.3964	0.0000	1.0000
F81G	39	-2548.8452	5342.0370	0.0000	1.0000
F81IG	40	-2548.8452	5348.3025	0.0000	1.0000
JC69G	36	-2563.5004	5352.5517	0.0000	1.0000
F81I	39	-2554.7038	5353.7544	0.0000	1.0000
JC69IG	37	-2563.5005	5358.8171	0.0000	1.0000
JC69I	36	-2569.8858	5365.3224	0.0000	1.0000
F81	38	-2598.4163	5434.9139	0.0000	1.0000
JC69	35	-2614.1159	5447.5174	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_18926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18926.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_18926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18926.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_18926.phylip = 1 - 526;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18926.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

