
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:40 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_17775.phylip" (19 taxa, 696 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2994.6321	6085.6334	0.5218	0.5218
GTRG	44	-2995.9184	6085.9198	0.4522	0.9740
HKYIG	41	-3002.8380	6092.9421	0.0135	0.9875
HKYG	40	-3004.0439	6093.0955	0.0125	1.0000
GTRI	44	-3011.5834	6117.2497	0.0000	1.0000
HKYI	40	-3016.8875	6118.7826	0.0000	1.0000
K2PG	37	-3026.5127	6131.2989	0.0000	1.0000
K2PIG	38	-3025.6286	6131.7686	0.0000	1.0000
SYMG	41	-3023.1978	6133.6617	0.0000	1.0000
SYMIG	42	-3022.4096	6134.3506	0.0000	1.0000
K2PI	37	-3036.7383	6151.7501	0.0000	1.0000
SYMI	41	-3033.1531	6153.5722	0.0000	1.0000
GTR	43	-3101.6165	6295.0367	0.0000	1.0000
HKY	39	-3106.7449	6296.2458	0.0000	1.0000
F81G	39	-3115.6165	6313.9891	0.0000	1.0000
F81IG	40	-3116.2378	6317.4832	0.0000	1.0000
SYM	40	-3123.5231	6332.0539	0.0000	1.0000
F81I	39	-3124.6875	6332.1311	0.0000	1.0000
K2P	36	-3128.1048	6332.2521	0.0000	1.0000
JC69G	36	-3128.7184	6333.4792	0.0000	1.0000
JC69IG	37	-3129.7283	6337.7302	0.0000	1.0000
JC69I	36	-3137.0874	6350.2174	0.0000	1.0000
F81	38	-3209.4519	6499.4152	0.0000	1.0000
JC69	35	-3222.5199	6518.8579	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2994.6321	6079.2642	0.5624	0.5624
GTRG	44	-2995.9184	6079.8369	0.4224	0.9848
HKYIG	41	-3002.8380	6087.6761	0.0084	0.9932
HKYG	40	-3004.0439	6088.0878	0.0068	1.0000
GTRI	44	-3011.5834	6111.1667	0.0000	1.0000
HKYI	40	-3016.8875	6113.7749	0.0000	1.0000
K2PG	37	-3026.5127	6127.0253	0.0000	1.0000
K2PIG	38	-3025.6286	6127.2572	0.0000	1.0000
SYMG	41	-3023.1978	6128.3956	0.0000	1.0000
SYMIG	42	-3022.4096	6128.8192	0.0000	1.0000
K2PI	37	-3036.7383	6147.4766	0.0000	1.0000
SYMI	41	-3033.1531	6148.3062	0.0000	1.0000
GTR	43	-3101.6165	6289.2330	0.0000	1.0000
HKY	39	-3106.7449	6291.4897	0.0000	1.0000
F81G	39	-3115.6165	6309.2330	0.0000	1.0000
F81IG	40	-3116.2378	6312.4756	0.0000	1.0000
SYM	40	-3123.5231	6327.0462	0.0000	1.0000
F81I	39	-3124.6875	6327.3750	0.0000	1.0000
K2P	36	-3128.1048	6328.2096	0.0000	1.0000
JC69G	36	-3128.7184	6329.4368	0.0000	1.0000
JC69IG	37	-3129.7283	6333.4567	0.0000	1.0000
JC69I	36	-3137.0874	6346.1749	0.0000	1.0000
F81	38	-3209.4519	6494.9037	0.0000	1.0000
JC69	35	-3222.5199	6515.0397	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3004.0439	6269.9018	0.8814	0.8814
HKYIG	41	-3002.8380	6274.0354	0.1116	0.9930
GTRG	44	-2995.9184	6279.8322	0.0061	0.9992
GTRIG	45	-2994.6321	6283.8049	0.0008	1.0000
K2PG	37	-3026.5127	6295.2033	0.0000	1.0000
HKYI	40	-3016.8875	6295.5889	0.0000	1.0000
K2PIG	38	-3025.6286	6299.9805	0.0000	1.0000
GTRI	44	-3011.5834	6311.1621	0.0000	1.0000
SYMG	41	-3023.1978	6314.7549	0.0000	1.0000
K2PI	37	-3036.7383	6315.6545	0.0000	1.0000
SYMIG	42	-3022.4096	6319.7239	0.0000	1.0000
SYMI	41	-3033.1531	6334.6655	0.0000	1.0000
HKY	39	-3106.7449	6468.7583	0.0000	1.0000
GTR	43	-3101.6165	6484.6831	0.0000	1.0000
F81G	39	-3115.6165	6486.5017	0.0000	1.0000
K2P	36	-3128.1048	6491.8422	0.0000	1.0000
JC69G	36	-3128.7184	6493.0693	0.0000	1.0000
F81IG	40	-3116.2378	6494.2896	0.0000	1.0000
JC69IG	37	-3129.7283	6501.6346	0.0000	1.0000
F81I	39	-3124.6875	6504.6436	0.0000	1.0000
SYM	40	-3123.5231	6508.8602	0.0000	1.0000
JC69I	36	-3137.0874	6509.8075	0.0000	1.0000
F81	38	-3209.4519	6667.6270	0.0000	1.0000
JC69	35	-3222.5199	6674.1270	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_17775.phylip = 1 - 696;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17775.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_17775.phylip = 1 - 696;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17775.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17775.phylip = 1 - 696;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17775.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

