
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:30 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_1989.phylip" (19 taxa, 687 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	-2243.9180	4582.0042	0.3374	0.3374
HKYG	40	-2248.6528	4582.3829	0.2792	0.6165
GTRIG	45	-2243.3655	4583.1897	0.1865	0.8030
HKYIG	41	-2248.1126	4583.5647	0.1546	0.9576
HKYI	40	-2251.1885	4587.4544	0.0221	0.9797
GTRI	44	-2246.7294	4587.6270	0.0203	1.0000
SYMIG	42	-2296.5056	4682.6199	0.0000	1.0000
SYMG	41	-2297.7288	4682.7971	0.0000	1.0000
SYMI	41	-2301.3233	4689.9861	0.0000	1.0000
GTR	43	-2299.4356	4690.7561	0.0000	1.0000
K2PG	37	-2306.5189	4691.3706	0.0000	1.0000
K2PIG	38	-2305.4149	4691.4038	0.0000	1.0000
HKY	39	-2306.2322	4695.2867	0.0000	1.0000
K2PI	37	-2309.4068	4697.1464	0.0000	1.0000
F81G	39	-2307.2051	4697.2325	0.0000	1.0000
F81IG	40	-2306.2000	4697.4774	0.0000	1.0000
F81I	39	-2310.1168	4703.0559	0.0000	1.0000
JC69G	36	-2350.3003	4776.6991	0.0000	1.0000
JC69IG	37	-2349.5939	4777.5205	0.0000	1.0000
JC69I	36	-2352.9666	4782.0317	0.0000	1.0000
SYM	40	-2352.2872	4789.6519	0.0000	1.0000
K2P	36	-2357.7132	4791.5249	0.0000	1.0000
F81	38	-2357.5203	4795.6146	0.0000	1.0000
JC69	35	-2398.0157	4869.9024	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2243.9180	4575.8360	0.3969	0.3969
GTRIG	45	-2243.3655	4576.7310	0.2537	0.6505
HKYG	40	-2248.6528	4577.3055	0.1903	0.8409
HKYIG	41	-2248.1126	4578.2251	0.1202	0.9611
GTRI	44	-2246.7294	4581.4588	0.0239	0.9849
HKYI	40	-2251.1885	4582.3770	0.0151	1.0000
SYMIG	42	-2296.5056	4677.0112	0.0000	1.0000
SYMG	41	-2297.7288	4677.4576	0.0000	1.0000
SYMI	41	-2301.3233	4684.6466	0.0000	1.0000
GTR	43	-2299.4356	4684.8712	0.0000	1.0000
K2PIG	38	-2305.4149	4686.8297	0.0000	1.0000
K2PG	37	-2306.5189	4687.0378	0.0000	1.0000
HKY	39	-2306.2322	4690.4644	0.0000	1.0000
F81IG	40	-2306.2000	4692.4000	0.0000	1.0000
F81G	39	-2307.2051	4692.4102	0.0000	1.0000
K2PI	37	-2309.4068	4692.8136	0.0000	1.0000
F81I	39	-2310.1168	4698.2336	0.0000	1.0000
JC69G	36	-2350.3003	4772.6006	0.0000	1.0000
JC69IG	37	-2349.5939	4773.1877	0.0000	1.0000
JC69I	36	-2352.9666	4777.9332	0.0000	1.0000
SYM	40	-2352.2872	4784.5745	0.0000	1.0000
K2P	36	-2357.7132	4787.4264	0.0000	1.0000
F81	38	-2357.5203	4791.0406	0.0000	1.0000
JC69	35	-2398.0157	4866.0315	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2248.6528	4758.5989	0.8734	0.8734
HKYI	40	-2251.1885	4763.6704	0.0692	0.9426
HKYIG	41	-2248.1126	4764.0508	0.0572	0.9998
GTRG	44	-2243.9180	4775.2587	0.0002	1.0000
GTRIG	45	-2243.3655	4780.6861	0.0000	1.0000
GTRI	44	-2246.7294	4780.8815	0.0000	1.0000
K2PG	37	-2306.5189	4854.7341	0.0000	1.0000
K2PIG	38	-2305.4149	4859.0584	0.0000	1.0000
K2PI	37	-2309.4068	4860.5100	0.0000	1.0000
SYMG	41	-2297.7288	4863.2833	0.0000	1.0000
HKY	39	-2306.2322	4867.2254	0.0000	1.0000
SYMIG	42	-2296.5056	4867.3693	0.0000	1.0000
F81G	39	-2307.2051	4869.1713	0.0000	1.0000
SYMI	41	-2301.3233	4870.4723	0.0000	1.0000
F81IG	40	-2306.2000	4873.6933	0.0000	1.0000
F81I	39	-2310.1168	4874.9947	0.0000	1.0000
GTR	43	-2299.4356	4879.7616	0.0000	1.0000
JC69G	36	-2350.3003	4935.7647	0.0000	1.0000
JC69IG	37	-2349.5939	4940.8841	0.0000	1.0000
JC69I	36	-2352.9666	4941.0973	0.0000	1.0000
K2P	36	-2357.7132	4950.5904	0.0000	1.0000
F81	38	-2357.5203	4963.2693	0.0000	1.0000
SYM	40	-2352.2872	4965.8678	0.0000	1.0000
JC69	35	-2398.0157	5024.6632	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_1989.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1989.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_1989.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1989.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_1989.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1989.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

