
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:27 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_17281.phylip" (19 taxa, 531 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2519.9294	5136.0070	0.8658	0.8658
GTRIG	45	-2521.1069	5140.7498	0.0808	0.9466
HKYG	40	-2527.6045	5141.9030	0.0454	0.9920
HKYIG	41	-2528.3130	5145.6690	0.0069	0.9989
K2PG	37	-2535.4042	5150.5123	0.0006	0.9996
GTRI	44	-2528.2097	5152.5675	0.0002	0.9998
K2PIG	38	-2536.0911	5154.2066	0.0001	0.9999
SYMG	41	-2532.8134	5154.6697	0.0001	0.9999
SYMIG	42	-2532.5808	5156.5632	0.0000	1.0000
HKYI	40	-2535.1180	5156.9299	0.0000	1.0000
K2PI	37	-2542.9924	5165.6887	0.0000	1.0000
SYMI	41	-2540.3065	5169.6559	0.0000	1.0000
GTR	43	-2575.5699	5244.9098	0.0000	1.0000
HKY	39	-2585.7720	5255.8983	0.0000	1.0000
SYM	40	-2592.3451	5271.3841	0.0000	1.0000
K2P	36	-2597.1178	5271.6284	0.0000	1.0000
F81G	39	-2604.2218	5292.7980	0.0000	1.0000
F81IG	40	-2604.0406	5294.7751	0.0000	1.0000
JC69G	36	-2609.7013	5296.7953	0.0000	1.0000
JC69IG	37	-2609.5193	5298.7425	0.0000	1.0000
F81I	39	-2609.8711	5304.0965	0.0000	1.0000
JC69I	36	-2615.3845	5308.1618	0.0000	1.0000
F81	38	-2659.4169	5400.8582	0.0000	1.0000
JC69	35	-2666.4907	5408.0723	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2519.9294	5127.8588	0.8742	0.8742
GTRIG	45	-2521.1069	5132.2138	0.0991	0.9733
HKYG	40	-2527.6045	5135.2091	0.0222	0.9955
HKYIG	41	-2528.3130	5138.6260	0.0040	0.9995
GTRI	44	-2528.2097	5144.4193	0.0002	0.9997
K2PG	37	-2535.4042	5144.8085	0.0002	0.9999
SYMG	41	-2532.8134	5147.6268	0.0000	0.9999
K2PIG	38	-2536.0911	5148.1822	0.0000	1.0000
SYMIG	42	-2532.5808	5149.1616	0.0000	1.0000
HKYI	40	-2535.1180	5150.2360	0.0000	1.0000
K2PI	37	-2542.9924	5159.9848	0.0000	1.0000
SYMI	41	-2540.3065	5162.6129	0.0000	1.0000
GTR	43	-2575.5699	5237.1398	0.0000	1.0000
HKY	39	-2585.7720	5249.5439	0.0000	1.0000
SYM	40	-2592.3451	5264.6903	0.0000	1.0000
K2P	36	-2597.1178	5266.2357	0.0000	1.0000
F81G	39	-2604.2218	5286.4436	0.0000	1.0000
F81IG	40	-2604.0406	5288.0812	0.0000	1.0000
JC69G	36	-2609.7013	5291.4026	0.0000	1.0000
JC69IG	37	-2609.5193	5293.0386	0.0000	1.0000
F81I	39	-2609.8711	5297.7421	0.0000	1.0000
JC69I	36	-2615.3845	5302.7691	0.0000	1.0000
F81	38	-2659.4169	5394.8338	0.0000	1.0000
JC69	35	-2666.4907	5402.9814	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2535.4042	5302.9747	0.8145	0.8145
HKYG	40	-2527.6045	5306.1996	0.1624	0.9769
K2PIG	38	-2536.0911	5310.6232	0.0178	0.9947
HKYIG	41	-2528.3130	5313.8913	0.0035	0.9982
GTRG	44	-2519.9294	5315.9484	0.0012	0.9994
K2PI	37	-2542.9924	5318.1510	0.0004	0.9999
HKYI	40	-2535.1180	5321.2265	0.0001	0.9999
SYMG	41	-2532.8134	5322.8920	0.0000	1.0000
GTRIG	45	-2521.1069	5324.5781	0.0000	1.0000
SYMIG	42	-2532.5808	5328.7016	0.0000	1.0000
GTRI	44	-2528.2097	5332.5089	0.0000	1.0000
SYMI	41	-2540.3065	5337.8782	0.0000	1.0000
HKY	39	-2585.7720	5416.2597	0.0000	1.0000
K2P	36	-2597.1178	5420.1271	0.0000	1.0000
GTR	43	-2575.5699	5420.9546	0.0000	1.0000
SYM	40	-2592.3451	5435.6807	0.0000	1.0000
JC69G	36	-2609.7013	5445.2940	0.0000	1.0000
JC69IG	37	-2609.5193	5451.2048	0.0000	1.0000
F81G	39	-2604.2218	5453.1593	0.0000	1.0000
JC69I	36	-2615.3845	5456.6605	0.0000	1.0000
F81IG	40	-2604.0406	5459.0717	0.0000	1.0000
F81I	39	-2609.8711	5464.4578	0.0000	1.0000
JC69	35	-2666.4907	5552.5980	0.0000	1.0000
F81	38	-2659.4169	5557.2748	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_17281.phylip = 1 - 531;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17281.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_17281.phylip = 1 - 531;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17281.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17281.phylip = 1 - 531;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_17281.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

