
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:45 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_3386.phylip" (19 taxa, 837 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3617.2723	7327.5446	0.6731	0.6731
GTRIG	45	-3616.8896	7329.0131	0.3230	0.9961
GTRI	44	-3622.4373	7337.8746	0.0038	1.0000
HKYG	40	-3632.0491	7348.2188	0.0000	1.0000
HKYIG	41	-3631.5433	7349.4188	0.0000	1.0000
HKYI	40	-3636.0189	7356.1585	0.0000	1.0000
SYMG	41	-3647.2362	7380.8045	0.0000	1.0000
SYMIG	42	-3646.5325	7381.6140	0.0000	1.0000
K2PG	37	-3652.6866	7382.8926	0.0000	1.0000
K2PIG	38	-3652.0778	7383.8698	0.0000	1.0000
SYMI	41	-3650.0483	7386.4288	0.0000	1.0000
K2PI	37	-3655.9976	7389.5147	0.0000	1.0000
GTR	43	-3680.4863	7451.7444	0.0000	1.0000
HKY	39	-3695.0952	7472.1052	0.0000	1.0000
F81G	39	-3701.8798	7485.6743	0.0000	1.0000
F81IG	40	-3701.2847	7486.6900	0.0000	1.0000
F81I	39	-3704.7666	7491.4478	0.0000	1.0000
SYM	40	-3709.8636	7503.8478	0.0000	1.0000
K2P	36	-3716.5102	7508.3505	0.0000	1.0000
JC69G	36	-3717.6284	7510.5868	0.0000	1.0000
JC69IG	37	-3716.9654	7511.4503	0.0000	1.0000
JC69I	36	-3720.2140	7515.7579	0.0000	1.0000
F81	38	-3760.1504	7600.0150	0.0000	1.0000
JC69	35	-3776.3550	7625.8560	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3617.2723	7322.5446	0.6472	0.6472
GTRIG	45	-3616.8896	7323.7792	0.3491	0.9963
GTRI	44	-3622.4373	7332.8746	0.0037	1.0000
HKYG	40	-3632.0491	7344.0982	0.0000	1.0000
HKYIG	41	-3631.5433	7345.0867	0.0000	1.0000
HKYI	40	-3636.0189	7352.0379	0.0000	1.0000
SYMG	41	-3647.2362	7376.4724	0.0000	1.0000
SYMIG	42	-3646.5325	7377.0649	0.0000	1.0000
K2PG	37	-3652.6866	7379.3732	0.0000	1.0000
K2PIG	38	-3652.0778	7380.1556	0.0000	1.0000
SYMI	41	-3650.0483	7382.0967	0.0000	1.0000
K2PI	37	-3655.9976	7385.9953	0.0000	1.0000
GTR	43	-3680.4863	7446.9727	0.0000	1.0000
HKY	39	-3695.0952	7468.1905	0.0000	1.0000
F81G	39	-3701.8798	7481.7596	0.0000	1.0000
F81IG	40	-3701.2847	7482.5694	0.0000	1.0000
F81I	39	-3704.7666	7487.5331	0.0000	1.0000
SYM	40	-3709.8636	7499.7272	0.0000	1.0000
K2P	36	-3716.5102	7505.0205	0.0000	1.0000
JC69G	36	-3717.6284	7507.2568	0.0000	1.0000
JC69IG	37	-3716.9654	7507.9309	0.0000	1.0000
JC69I	36	-3720.2140	7512.4279	0.0000	1.0000
F81	38	-3760.1504	7596.3008	0.0000	1.0000
JC69	35	-3776.3550	7622.7099	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3617.2723	7530.6568	0.7437	0.7437
HKYG	40	-3632.0491	7533.2912	0.1992	0.9429
GTRIG	45	-3616.8896	7536.6213	0.0377	0.9806
HKYIG	41	-3631.5433	7539.0095	0.0114	0.9920
GTRI	44	-3622.4373	7540.9868	0.0042	0.9962
HKYI	40	-3636.0189	7541.2308	0.0038	1.0000
K2PG	37	-3652.6866	7554.3767	0.0000	1.0000
K2PIG	38	-3652.0778	7559.8889	0.0000	1.0000
K2PI	37	-3655.9976	7560.9988	0.0000	1.0000
SYMG	41	-3647.2362	7570.3952	0.0000	1.0000
SYMIG	42	-3646.5325	7575.7175	0.0000	1.0000
SYMI	41	-3650.0483	7576.0195	0.0000	1.0000
GTR	43	-3680.4863	7650.3551	0.0000	1.0000
HKY	39	-3695.0952	7652.6536	0.0000	1.0000
F81G	39	-3701.8798	7666.2228	0.0000	1.0000
F81IG	40	-3701.2847	7671.7624	0.0000	1.0000
F81I	39	-3704.7666	7671.9963	0.0000	1.0000
K2P	36	-3716.5102	7675.2942	0.0000	1.0000
JC69G	36	-3717.6284	7677.5305	0.0000	1.0000
JC69I	36	-3720.2140	7682.7016	0.0000	1.0000
JC69IG	37	-3716.9654	7682.9344	0.0000	1.0000
SYM	40	-3709.8636	7688.9202	0.0000	1.0000
F81	38	-3760.1504	7776.0341	0.0000	1.0000
JC69	35	-3776.3550	7788.2538	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_3386.phylip = 1 - 837;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3386.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_3386.phylip = 1 - 837;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3386.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3386.phylip = 1 - 837;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3386.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

