
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:09 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/chr1_32297.phylip" (19 taxa, 673 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2250.3720	4595.0498	0.4314	0.4314
GTRIG	45	-2249.5545	4595.7119	0.3098	0.7411
HKYIG	41	-2254.8690	4597.1960	0.1475	0.8886
GTRI	44	-2251.7333	4597.7724	0.1106	0.9992
HKYG	40	-2261.5572	4608.3043	0.0006	0.9998
HKYI	40	-2262.5117	4610.2133	0.0002	1.0000
GTR	43	-2285.2638	4662.5434	0.0000	1.0000
K2PG	37	-2293.5087	4665.4458	0.0000	1.0000
K2PIG	38	-2292.5604	4665.7959	0.0000	1.0000
SYMIG	42	-2289.1326	4667.9986	0.0000	1.0000
SYMG	41	-2290.4608	4668.3796	0.0000	1.0000
K2PI	37	-2299.3039	4677.0361	0.0000	1.0000
HKY	39	-2297.9010	4678.7309	0.0000	1.0000
SYMI	41	-2295.8070	4679.0720	0.0000	1.0000
F81G	39	-2324.6577	4732.2444	0.0000	1.0000
F81IG	40	-2323.8792	4732.9484	0.0000	1.0000
K2P	36	-2332.7798	4741.7483	0.0000	1.0000
SYM	40	-2328.4680	4742.1259	0.0000	1.0000
F81I	39	-2330.0273	4742.9836	0.0000	1.0000
JC69G	36	-2351.7353	4779.6593	0.0000	1.0000
JC69IG	37	-2350.8402	4780.1088	0.0000	1.0000
JC69I	36	-2357.1489	4790.4866	0.0000	1.0000
F81	38	-2360.4367	4801.5485	0.0000	1.0000
JC69	35	-2389.0882	4852.1324	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2250.3720	4588.7441	0.4321	0.4321
GTRIG	45	-2249.5545	4589.1091	0.3600	0.7921
GTRI	44	-2251.7333	4591.4667	0.1108	0.9028
HKYIG	41	-2254.8690	4591.7380	0.0967	0.9995
HKYG	40	-2261.5572	4603.1144	0.0003	0.9999
HKYI	40	-2262.5117	4605.0234	0.0001	1.0000
GTR	43	-2285.2638	4656.5275	0.0000	1.0000
K2PG	37	-2293.5087	4661.0174	0.0000	1.0000
K2PIG	38	-2292.5604	4661.1208	0.0000	1.0000
SYMIG	42	-2289.1326	4662.2652	0.0000	1.0000
SYMG	41	-2290.4608	4662.9216	0.0000	1.0000
K2PI	37	-2299.3039	4672.6077	0.0000	1.0000
SYMI	41	-2295.8070	4673.6140	0.0000	1.0000
HKY	39	-2297.9010	4673.8020	0.0000	1.0000
F81G	39	-2324.6577	4727.3155	0.0000	1.0000
F81IG	40	-2323.8792	4727.7585	0.0000	1.0000
SYM	40	-2328.4680	4736.9360	0.0000	1.0000
K2P	36	-2332.7798	4737.5596	0.0000	1.0000
F81I	39	-2330.0273	4738.0547	0.0000	1.0000
JC69G	36	-2351.7353	4775.4706	0.0000	1.0000
JC69IG	37	-2350.8402	4775.6805	0.0000	1.0000
JC69I	36	-2357.1489	4786.2979	0.0000	1.0000
F81	38	-2360.4367	4796.8734	0.0000	1.0000
JC69	35	-2389.0882	4848.1764	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2254.8690	4776.7196	0.9509	0.9509
HKYG	40	-2261.5572	4783.5842	0.0307	0.9816
HKYI	40	-2262.5117	4785.4932	0.0118	0.9934
GTRG	44	-2250.3720	4787.2609	0.0049	0.9983
GTRI	44	-2251.7333	4789.9835	0.0013	0.9996
GTRIG	45	-2249.5545	4792.1376	0.0004	1.0000
K2PG	37	-2293.5087	4827.9520	0.0000	1.0000
K2PIG	38	-2292.5604	4832.5671	0.0000	1.0000
K2PI	37	-2299.3039	4839.5423	0.0000	1.0000
SYMG	41	-2290.4608	4847.9032	0.0000	1.0000
HKY	39	-2297.9010	4849.7601	0.0000	1.0000
GTR	43	-2285.2638	4850.5326	0.0000	1.0000
SYMIG	42	-2289.1326	4851.7585	0.0000	1.0000
SYMI	41	-2295.8070	4858.5955	0.0000	1.0000
K2P	36	-2332.7798	4899.9825	0.0000	1.0000
F81G	39	-2324.6577	4903.2735	0.0000	1.0000
F81IG	40	-2323.8792	4908.2283	0.0000	1.0000
F81I	39	-2330.0273	4914.0128	0.0000	1.0000
SYM	40	-2328.4680	4917.4058	0.0000	1.0000
JC69G	36	-2351.7353	4937.8935	0.0000	1.0000
JC69IG	37	-2350.8402	4942.6150	0.0000	1.0000
JC69I	36	-2357.1489	4948.7207	0.0000	1.0000
F81	38	-2360.4367	4968.3197	0.0000	1.0000
JC69	35	-2389.0882	5006.0874	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/chr1_32297.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32297.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/chr1_32297.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32297.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32297.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32297.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;


-------------------------------------------------------------
End of Output

