
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:02 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_31767.phylip" (19 taxa, 684 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3022.0444	6138.2859	0.8232	0.8232
GTRIG	45	-3022.5860	6141.6609	0.1523	0.9754
GTRI	44	-3025.8025	6145.8021	0.0192	0.9946
HKYG	40	-3031.9177	6148.9364	0.0040	0.9987
HKYIG	41	-3031.9174	6151.1993	0.0013	0.9999
HKYI	40	-3036.2653	6157.6317	0.0001	1.0000
SYMG	41	-3038.1294	6163.6233	0.0000	1.0000
K2PG	37	-3043.7123	6165.7776	0.0000	1.0000
SYMIG	42	-3038.1292	6165.8932	0.0000	1.0000
K2PIG	38	-3043.7138	6168.0229	0.0000	1.0000
SYMI	41	-3043.8534	6175.0713	0.0000	1.0000
K2PI	37	-3049.4774	6177.3078	0.0000	1.0000
F81G	39	-3121.0687	6324.9822	0.0000	1.0000
GTR	43	-3116.7028	6325.3181	0.0000	1.0000
F81IG	40	-3121.1533	6327.4076	0.0000	1.0000
F81I	39	-3123.8331	6330.5108	0.0000	1.0000
HKY	39	-3126.8434	6336.5315	0.0000	1.0000
JC69G	36	-3130.9269	6337.9713	0.0000	1.0000
JC69IG	37	-3131.0049	6340.3627	0.0000	1.0000
JC69I	36	-3134.5297	6345.1769	0.0000	1.0000
SYM	40	-3133.3733	6351.8476	0.0000	1.0000
K2P	36	-3139.1293	6354.3761	0.0000	1.0000
F81	38	-3207.8993	6496.3939	0.0000	1.0000
JC69	35	-3218.2557	6510.4003	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3022.0444	6132.0888	0.8056	0.8056
GTRIG	45	-3022.5860	6135.1719	0.1724	0.9781
GTRI	44	-3025.8025	6139.6050	0.0188	0.9969
HKYG	40	-3031.9177	6143.8353	0.0023	0.9991
HKYIG	41	-3031.9174	6145.8348	0.0008	1.0000
HKYI	40	-3036.2653	6152.5306	0.0000	1.0000
SYMG	41	-3038.1294	6158.2589	0.0000	1.0000
SYMIG	42	-3038.1292	6160.2583	0.0000	1.0000
K2PG	37	-3043.7123	6161.4246	0.0000	1.0000
K2PIG	38	-3043.7138	6163.4276	0.0000	1.0000
SYMI	41	-3043.8534	6169.7068	0.0000	1.0000
K2PI	37	-3049.4774	6172.9548	0.0000	1.0000
GTR	43	-3116.7028	6319.4056	0.0000	1.0000
F81G	39	-3121.0687	6320.1375	0.0000	1.0000
F81IG	40	-3121.1533	6322.3065	0.0000	1.0000
F81I	39	-3123.8331	6325.6661	0.0000	1.0000
HKY	39	-3126.8434	6331.6868	0.0000	1.0000
JC69G	36	-3130.9269	6333.8538	0.0000	1.0000
JC69IG	37	-3131.0049	6336.0098	0.0000	1.0000
JC69I	36	-3134.5297	6341.0594	0.0000	1.0000
SYM	40	-3133.3733	6346.7465	0.0000	1.0000
K2P	36	-3139.1293	6350.2586	0.0000	1.0000
F81	38	-3207.8993	6491.7986	0.0000	1.0000
JC69	35	-3218.2557	6506.5115	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3031.9177	6324.9537	0.8096	0.8096
K2PG	37	-3043.7123	6328.9591	0.1093	0.9189
GTRG	44	-3022.0444	6331.3189	0.0336	0.9525
HKYIG	41	-3031.9174	6331.4811	0.0310	0.9834
HKYI	40	-3036.2653	6333.6489	0.0105	0.9939
K2PIG	38	-3043.7138	6335.4900	0.0042	0.9981
GTRI	44	-3025.8025	6338.8351	0.0008	0.9988
GTRIG	45	-3022.5860	6338.9300	0.0007	0.9996
K2PI	37	-3049.4774	6340.4893	0.0003	0.9999
SYMG	41	-3038.1294	6343.9051	0.0001	1.0000
SYMIG	42	-3038.1292	6350.4325	0.0000	1.0000
SYMI	41	-3043.8534	6355.3531	0.0000	1.0000
F81G	39	-3121.0687	6496.7279	0.0000	1.0000
JC69G	36	-3130.9269	6496.8603	0.0000	1.0000
F81I	39	-3123.8331	6502.2565	0.0000	1.0000
F81IG	40	-3121.1533	6503.4248	0.0000	1.0000
JC69IG	37	-3131.0049	6503.5442	0.0000	1.0000
JC69I	36	-3134.5297	6504.0659	0.0000	1.0000
HKY	39	-3126.8434	6508.2771	0.0000	1.0000
K2P	36	-3139.1293	6513.2651	0.0000	1.0000
GTR	43	-3116.7028	6514.1078	0.0000	1.0000
SYM	40	-3133.3733	6527.8648	0.0000	1.0000
F81	38	-3207.8993	6663.8610	0.0000	1.0000
JC69	35	-3218.2557	6664.9900	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_31767.phylip = 1 - 684;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31767.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_31767.phylip = 1 - 684;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31767.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31767.phylip = 1 - 684;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_31767.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

