
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:06 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_5301.phylip" (19 taxa, 1176 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-3577.0173	7245.5360	0.4506	0.4506
GTRG	44	-3577.4764	7246.4540	0.2847	0.7353
GTRIG	45	-3576.6368	7246.9374	0.2236	0.9589
HKYG	40	-3584.3405	7251.5709	0.0220	0.9809
HKYIG	41	-3583.5300	7252.0970	0.0169	0.9979
HKYI	40	-3586.6767	7256.2432	0.0021	1.0000
HKY	39	-3633.7459	7348.2383	0.0000	1.0000
SYMIG	42	-3633.7276	7354.6433	0.0000	1.0000
K2PI	37	-3639.6901	7355.8512	0.0000	1.0000
K2PG	37	-3640.1231	7356.7173	0.0000	1.0000
K2PIG	38	-3639.2281	7357.0631	0.0000	1.0000
SYMI	41	-3636.6716	7358.3802	0.0000	1.0000
SYMG	41	-3637.0020	7359.0410	0.0000	1.0000
GTR	43	-3638.3470	7366.0368	0.0000	1.0000
F81G	39	-3659.1678	7399.0821	0.0000	1.0000
F81I	39	-3661.2937	7403.3339	0.0000	1.0000
F81IG	40	-3667.3012	7417.4923	0.0000	1.0000
K2P	36	-3696.8993	7468.1375	0.0000	1.0000
SYM	40	-3693.1910	7469.2718	0.0000	1.0000
JC69G	36	-3706.7693	7487.8775	0.0000	1.0000
JC69IG	37	-3706.1562	7488.7834	0.0000	1.0000
JC69I	36	-3708.9592	7492.2574	0.0000	1.0000
F81	38	-3707.6900	7493.9868	0.0000	1.0000
JC69	35	-3754.6350	7581.4805	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-3577.0173	7242.0346	0.4465	0.4465
GTRG	44	-3577.4764	7242.9527	0.2822	0.7287
GTRIG	45	-3576.6368	7243.2737	0.2403	0.9690
HKYG	40	-3584.3405	7248.6810	0.0161	0.9851
HKYIG	41	-3583.5300	7249.0600	0.0133	0.9984
HKYI	40	-3586.6767	7253.3534	0.0016	1.0000
HKY	39	-3633.7459	7345.4918	0.0000	1.0000
SYMIG	42	-3633.7276	7351.4553	0.0000	1.0000
K2PI	37	-3639.6901	7353.3802	0.0000	1.0000
K2PG	37	-3640.1231	7354.2463	0.0000	1.0000
K2PIG	38	-3639.2281	7354.4562	0.0000	1.0000
SYMI	41	-3636.6716	7355.3431	0.0000	1.0000
SYMG	41	-3637.0020	7356.0039	0.0000	1.0000
GTR	43	-3638.3470	7362.6941	0.0000	1.0000
F81G	39	-3659.1678	7396.3356	0.0000	1.0000
F81I	39	-3661.2937	7400.5874	0.0000	1.0000
F81IG	40	-3667.3012	7414.6024	0.0000	1.0000
K2P	36	-3696.8993	7465.7986	0.0000	1.0000
SYM	40	-3693.1910	7466.3819	0.0000	1.0000
JC69G	36	-3706.7693	7485.5386	0.0000	1.0000
JC69IG	37	-3706.1562	7486.3124	0.0000	1.0000
JC69I	36	-3708.9592	7489.9185	0.0000	1.0000
F81	38	-3707.6900	7491.3799	0.0000	1.0000
JC69	35	-3754.6350	7579.2700	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3584.3405	7451.4760	0.8590	0.8590
HKYI	40	-3586.6767	7456.1483	0.0831	0.9421
HKYIG	41	-3583.5300	7456.9248	0.0563	0.9984
GTRI	44	-3577.0173	7465.1091	0.0009	0.9994
GTRG	44	-3577.4764	7466.0272	0.0006	1.0000
GTRIG	45	-3576.6368	7471.4180	0.0000	1.0000
K2PI	37	-3639.6901	7540.9655	0.0000	1.0000
K2PG	37	-3640.1231	7541.8316	0.0000	1.0000
HKY	39	-3633.7459	7543.2169	0.0000	1.0000
K2PIG	38	-3639.2281	7547.1114	0.0000	1.0000
SYMI	41	-3636.6716	7563.2080	0.0000	1.0000
SYMG	41	-3637.0020	7563.8688	0.0000	1.0000
SYMIG	42	-3633.7276	7564.3900	0.0000	1.0000
GTR	43	-3638.3470	7580.6986	0.0000	1.0000
F81G	39	-3659.1678	7594.0607	0.0000	1.0000
F81I	39	-3661.2937	7598.3125	0.0000	1.0000
F81IG	40	-3667.3012	7617.3974	0.0000	1.0000
K2P	36	-3696.8993	7648.3140	0.0000	1.0000
JC69G	36	-3706.7693	7668.0540	0.0000	1.0000
SYM	40	-3693.1910	7669.1769	0.0000	1.0000
JC69I	36	-3708.9592	7672.4339	0.0000	1.0000
JC69IG	37	-3706.1562	7673.8978	0.0000	1.0000
F81	38	-3707.6900	7684.0351	0.0000	1.0000
JC69	35	-3754.6350	7756.7156	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5301.phylip = 1 - 1176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5301.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5301.phylip = 1 - 1176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5301.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) 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/chr1_5301.phylip = 1 - 1176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5301.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

