
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:25 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_29922.phylip" (19 taxa, 766 characters)

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


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	-2565.2746	5226.2992	0.9094	0.9094
GTRG	44	-2568.7095	5230.9114	0.0906	1.0000
GTRI	44	-2578.8239	5251.1402	0.0000	1.0000
HKYIG	41	-2586.6623	5260.0815	0.0000	1.0000
HKYG	40	-2588.5705	5261.6651	0.0000	1.0000
HKYI	40	-2594.2805	5273.0851	0.0000	1.0000
SYMIG	42	-2619.3994	5327.7948	0.0000	1.0000
K2PIG	38	-2624.2427	5328.5624	0.0000	1.0000
SYMG	41	-2621.5080	5329.7729	0.0000	1.0000
K2PG	37	-2626.0561	5329.9748	0.0000	1.0000
K2PI	37	-2630.1677	5338.1980	0.0000	1.0000
SYMI	41	-2626.2043	5339.1654	0.0000	1.0000
GTR	43	-2645.9253	5383.0916	0.0000	1.0000
F81IG	40	-2652.9949	5390.5139	0.0000	1.0000
F81G	39	-2655.0016	5392.3008	0.0000	1.0000
F81I	39	-2660.0525	5402.4026	0.0000	1.0000
HKY	39	-2662.4614	5407.2204	0.0000	1.0000
JC69G	36	-2682.6226	5440.8996	0.0000	1.0000
JC69IG	37	-2682.0959	5442.0544	0.0000	1.0000
JC69I	36	-2688.3610	5452.3763	0.0000	1.0000
SYM	40	-2696.0090	5476.5421	0.0000	1.0000
K2P	36	-2701.6575	5478.9694	0.0000	1.0000
F81	38	-2726.1583	5532.3936	0.0000	1.0000
JC69	35	-2756.4241	5586.3002	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2565.2746	5220.5492	0.9194	0.9194
GTRG	44	-2568.7095	5225.4190	0.0806	1.0000
GTRI	44	-2578.8239	5245.6478	0.0000	1.0000
HKYIG	41	-2586.6623	5255.3246	0.0000	1.0000
HKYG	40	-2588.5705	5257.1410	0.0000	1.0000
HKYI	40	-2594.2805	5268.5610	0.0000	1.0000
SYMIG	42	-2619.3994	5322.7989	0.0000	1.0000
K2PIG	38	-2624.2427	5324.4854	0.0000	1.0000
SYMG	41	-2621.5080	5325.0160	0.0000	1.0000
K2PG	37	-2626.0561	5326.1122	0.0000	1.0000
K2PI	37	-2630.1677	5334.3354	0.0000	1.0000
SYMI	41	-2626.2043	5334.4085	0.0000	1.0000
GTR	43	-2645.9253	5377.8506	0.0000	1.0000
F81IG	40	-2652.9949	5385.9898	0.0000	1.0000
F81G	39	-2655.0016	5388.0032	0.0000	1.0000
F81I	39	-2660.0525	5398.1051	0.0000	1.0000
HKY	39	-2662.4614	5402.9229	0.0000	1.0000
JC69G	36	-2682.6226	5437.2453	0.0000	1.0000
JC69IG	37	-2682.0959	5438.1917	0.0000	1.0000
JC69I	36	-2688.3610	5448.7220	0.0000	1.0000
SYM	40	-2696.0090	5472.0179	0.0000	1.0000
K2P	36	-2701.6575	5475.3151	0.0000	1.0000
F81	38	-2726.1583	5528.3165	0.0000	1.0000
JC69	35	-2756.4241	5582.8481	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRIG	45	-2565.2746	5429.4024	0.5281	0.5281
GTRG	44	-2568.7095	5429.6310	0.4711	0.9992
HKYG	40	-2588.5705	5442.7883	0.0007	0.9998
HKYIG	41	-2586.6623	5445.6131	0.0002	1.0000
GTRI	44	-2578.8239	5449.8599	0.0000	1.0000
HKYI	40	-2594.2805	5454.2082	0.0000	1.0000
K2PG	37	-2626.0561	5497.8359	0.0000	1.0000
K2PIG	38	-2624.2427	5500.8503	0.0000	1.0000
K2PI	37	-2630.1677	5506.0591	0.0000	1.0000
SYMG	41	-2621.5080	5515.3045	0.0000	1.0000
SYMIG	42	-2619.3994	5517.7286	0.0000	1.0000
SYMI	41	-2626.2043	5524.6970	0.0000	1.0000
F81G	39	-2655.0016	5569.0093	0.0000	1.0000
F81IG	40	-2652.9949	5571.6371	0.0000	1.0000
GTR	43	-2645.9253	5577.4214	0.0000	1.0000
F81I	39	-2660.0525	5579.1112	0.0000	1.0000
HKY	39	-2662.4614	5583.9290	0.0000	1.0000
JC69G	36	-2682.6226	5604.3278	0.0000	1.0000
JC69IG	37	-2682.0959	5609.9155	0.0000	1.0000
JC69I	36	-2688.3610	5615.8046	0.0000	1.0000
K2P	36	-2701.6575	5642.3977	0.0000	1.0000
SYM	40	-2696.0090	5657.6652	0.0000	1.0000
F81	38	-2726.1583	5704.6815	0.0000	1.0000
JC69	35	-2756.4241	5745.2895	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/chr1_29922.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29922.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/chr1_29922.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29922.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 (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29922.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_29922.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;


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End of Output

