
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:07 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/chr11_3447.phylip" (19 taxa, 1034 characters)

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


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	-3464.5804	7023.3510	0.8818	0.8818
GTRG	44	-3467.6833	7027.3706	0.1182	1.0000
GTRI	44	-3477.8946	7047.7933	0.0000	1.0000
HKYG	40	-3482.4651	7048.2333	0.0000	1.0000
HKYIG	41	-3482.4162	7050.3042	0.0000	1.0000
SYMG	41	-3491.2179	7067.9076	0.0000	1.0000
HKYI	40	-3493.0576	7069.4184	0.0000	1.0000
SYMIG	42	-3491.0922	7069.8293	0.0000	1.0000
SYMI	41	-3501.2952	7088.0621	0.0000	1.0000
K2PG	37	-3509.5667	7095.9567	0.0000	1.0000
K2PIG	38	-3509.5225	7098.0239	0.0000	1.0000
K2PI	37	-3520.7407	7118.3048	0.0000	1.0000
HKY	39	-3548.1274	7177.3937	0.0000	1.0000
GTR	43	-3545.4926	7180.8074	0.0000	1.0000
F81G	39	-3550.0436	7181.2261	0.0000	1.0000
F81IG	40	-3549.9235	7183.1500	0.0000	1.0000
SYM	40	-3555.9873	7195.2778	0.0000	1.0000
F81I	39	-3559.4961	7200.1311	0.0000	1.0000
JC69G	36	-3588.3462	7251.3645	0.0000	1.0000
JC69IG	37	-3588.2392	7253.3018	0.0000	1.0000
JC69I	36	-3597.0525	7268.7769	0.0000	1.0000
K2P	36	-3597.1879	7269.0479	0.0000	1.0000
F81	38	-3608.1237	7295.2262	0.0000	1.0000
JC69	35	-3647.5164	7367.5578	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3464.5804	7019.1607	0.8912	0.8912
GTRG	44	-3467.6833	7023.3665	0.1088	1.0000
GTRI	44	-3477.8946	7043.7893	0.0000	1.0000
HKYG	40	-3482.4651	7044.9302	0.0000	1.0000
HKYIG	41	-3482.4162	7046.8324	0.0000	1.0000
SYMG	41	-3491.2179	7064.4358	0.0000	1.0000
HKYI	40	-3493.0576	7066.1153	0.0000	1.0000
SYMIG	42	-3491.0922	7066.1845	0.0000	1.0000
SYMI	41	-3501.2952	7084.5903	0.0000	1.0000
K2PG	37	-3509.5667	7093.1334	0.0000	1.0000
K2PIG	38	-3509.5225	7095.0450	0.0000	1.0000
K2PI	37	-3520.7407	7115.4815	0.0000	1.0000
HKY	39	-3548.1274	7174.2548	0.0000	1.0000
GTR	43	-3545.4926	7176.9851	0.0000	1.0000
F81G	39	-3550.0436	7178.0873	0.0000	1.0000
F81IG	40	-3549.9235	7179.8469	0.0000	1.0000
SYM	40	-3555.9873	7191.9747	0.0000	1.0000
F81I	39	-3559.4961	7196.9923	0.0000	1.0000
JC69G	36	-3588.3462	7248.6924	0.0000	1.0000
JC69IG	37	-3588.2392	7250.4785	0.0000	1.0000
JC69I	36	-3597.0525	7266.1049	0.0000	1.0000
K2P	36	-3597.1879	7266.3759	0.0000	1.0000
F81	38	-3608.1237	7292.2473	0.0000	1.0000
JC69	35	-3647.5164	7365.0328	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3467.6833	7240.7789	0.4734	0.4734
GTRIG	45	-3464.5804	7241.5143	0.3277	0.8011
HKYG	40	-3482.4651	7242.5778	0.1926	0.9937
HKYIG	41	-3482.4162	7249.4212	0.0063	1.0000
GTRI	44	-3477.8946	7261.2016	0.0000	1.0000
HKYI	40	-3493.0576	7263.7629	0.0000	1.0000
SYMG	41	-3491.2179	7267.0246	0.0000	1.0000
SYMIG	42	-3491.0922	7273.7145	0.0000	1.0000
K2PG	37	-3509.5667	7275.9575	0.0000	1.0000
K2PIG	38	-3509.5225	7282.8102	0.0000	1.0000
SYMI	41	-3501.2952	7287.1791	0.0000	1.0000
K2PI	37	-3520.7407	7298.3055	0.0000	1.0000
HKY	39	-3548.1274	7366.9613	0.0000	1.0000
F81G	39	-3550.0436	7370.7937	0.0000	1.0000
F81IG	40	-3549.9235	7377.4945	0.0000	1.0000
GTR	43	-3545.4926	7389.4563	0.0000	1.0000
SYM	40	-3555.9873	7389.6223	0.0000	1.0000
F81I	39	-3559.4961	7389.6987	0.0000	1.0000
JC69G	36	-3588.3462	7426.5753	0.0000	1.0000
JC69IG	37	-3588.2392	7433.3025	0.0000	1.0000
JC69I	36	-3597.0525	7443.9878	0.0000	1.0000
K2P	36	-3597.1879	7444.2587	0.0000	1.0000
F81	38	-3608.1237	7480.0125	0.0000	1.0000
JC69	35	-3647.5164	7537.9744	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/chr11_3447.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3447.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/chr11_3447.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3447.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3447.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3447.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;


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End of Output

