
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:59 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_23668.phylip" (19 taxa, 809 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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
GTRIG	45	-2240.5348	4576.4956	0.6277	0.6277
HKYIG	41	-2245.7066	4577.9034	0.3105	0.9382
GTRG	44	-2245.0087	4583.2006	0.0220	0.9602
GTRI	44	-2245.1867	4583.5566	0.0184	0.9785
HKYI	40	-2250.1716	4584.6140	0.0108	0.9894
HKYG	40	-2250.1912	4584.6533	0.0106	1.0000
K2PIG	38	-2282.1996	4644.2485	0.0000	1.0000
F81G	39	-2282.1647	4646.3867	0.0000	1.0000
SYMIG	42	-2279.1762	4647.0678	0.0000	1.0000
K2PI	37	-2286.4892	4650.6256	0.0000	1.0000
K2PG	37	-2286.7320	4651.1113	0.0000	1.0000
SYMI	41	-2283.3427	4653.1756	0.0000	1.0000
SYMG	41	-2283.5387	4653.5676	0.0000	1.0000
F81IG	40	-2291.9990	4668.2688	0.0000	1.0000
F81I	39	-2295.9170	4673.8912	0.0000	1.0000
GTR	43	-2300.2886	4691.5235	0.0000	1.0000
HKY	39	-2305.3556	4692.7684	0.0000	1.0000
JC69G	36	-2312.7791	4701.0090	0.0000	1.0000
JC69IG	37	-2322.5656	4722.7784	0.0000	1.0000
JC69I	36	-2326.6019	4728.6545	0.0000	1.0000
K2P	36	-2341.5003	4758.4514	0.0000	1.0000
SYM	40	-2338.0423	4760.3555	0.0000	1.0000
F81	38	-2365.1485	4810.1465	0.0000	1.0000
JC69	35	-2379.1260	4831.5121	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2240.5348	4571.0697	0.7215	0.7215
HKYIG	41	-2245.7066	4573.4132	0.2235	0.9451
GTRG	44	-2245.0087	4578.0173	0.0224	0.9674
GTRI	44	-2245.1867	4578.3734	0.0187	0.9862
HKYI	40	-2250.1716	4580.3432	0.0070	0.9931
HKYG	40	-2250.1912	4580.3825	0.0069	1.0000
K2PIG	38	-2282.1996	4640.3991	0.0000	1.0000
F81G	39	-2282.1647	4642.3294	0.0000	1.0000
SYMIG	42	-2279.1762	4642.3524	0.0000	1.0000
K2PI	37	-2286.4892	4646.9784	0.0000	1.0000
K2PG	37	-2286.7320	4647.4641	0.0000	1.0000
SYMI	41	-2283.3427	4648.6853	0.0000	1.0000
SYMG	41	-2283.5387	4649.0773	0.0000	1.0000
F81IG	40	-2291.9990	4663.9980	0.0000	1.0000
F81I	39	-2295.9170	4669.8339	0.0000	1.0000
GTR	43	-2300.2886	4686.5771	0.0000	1.0000
HKY	39	-2305.3556	4688.7112	0.0000	1.0000
JC69G	36	-2312.7791	4697.5582	0.0000	1.0000
JC69IG	37	-2322.5656	4719.1312	0.0000	1.0000
JC69I	36	-2326.6019	4725.2037	0.0000	1.0000
K2P	36	-2341.5003	4755.0006	0.0000	1.0000
SYM	40	-2338.0423	4756.0847	0.0000	1.0000
F81	38	-2365.1485	4806.2971	0.0000	1.0000
JC69	35	-2379.1260	4828.2521	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2245.7066	4765.9410	0.6066	0.6066
HKYI	40	-2250.1716	4768.1752	0.1985	0.8051
HKYG	40	-2250.1912	4768.2145	0.1946	0.9997
GTRIG	45	-2240.5348	4782.3806	0.0002	0.9999
GTRG	44	-2245.0087	4784.6325	0.0001	1.0000
GTRI	44	-2245.1867	4784.9885	0.0000	1.0000
K2PIG	38	-2282.1996	4818.8395	0.0000	1.0000
K2PI	37	-2286.4892	4820.7229	0.0000	1.0000
K2PG	37	-2286.7320	4821.2086	0.0000	1.0000
F81G	39	-2282.1647	4825.4656	0.0000	1.0000
SYMIG	42	-2279.1762	4839.5760	0.0000	1.0000
SYMI	41	-2283.3427	4841.2131	0.0000	1.0000
SYMG	41	-2283.5387	4841.6051	0.0000	1.0000
F81IG	40	-2291.9990	4851.8299	0.0000	1.0000
F81I	39	-2295.9170	4852.9701	0.0000	1.0000
JC69G	36	-2312.7791	4866.6070	0.0000	1.0000
HKY	39	-2305.3556	4871.8473	0.0000	1.0000
GTR	43	-2300.2886	4888.4965	0.0000	1.0000
JC69IG	37	-2322.5656	4892.8757	0.0000	1.0000
JC69I	36	-2326.6019	4894.2525	0.0000	1.0000
K2P	36	-2341.5003	4924.0494	0.0000	1.0000
SYM	40	-2338.0423	4943.9166	0.0000	1.0000
F81	38	-2365.1485	4984.7375	0.0000	1.0000
JC69	35	-2379.1260	4992.6050	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/chr2_23668.phylip = 1 - 809;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23668.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 (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23668.phylip = 1 - 809;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23668.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 BIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23668.phylip = 1 - 809;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23668.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;


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End of Output

