
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:30 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/chrZ_13094.phylip" (19 taxa, 900 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	-3655.6057	7403.8429	0.7891	0.7891
GTRIG	45	-3655.9682	7406.7843	0.1813	0.9704
GTRI	44	-3659.2371	7411.1057	0.0209	0.9913
HKYG	40	-3664.7821	7413.3826	0.0067	0.9980
HKYIG	41	-3664.9688	7415.9516	0.0019	0.9998
HKYI	40	-3668.5654	7420.9491	0.0002	1.0000
F81IG	40	-3717.1837	7518.1858	0.0000	1.0000
F81G	39	-3718.5939	7518.8157	0.0000	1.0000
F81I	39	-3719.8426	7521.3132	0.0000	1.0000
GTR	43	-3717.9712	7526.3630	0.0000	1.0000
HKY	39	-3726.6913	7535.0104	0.0000	1.0000
SYMG	41	-3727.6312	7541.2764	0.0000	1.0000
K2PG	37	-3734.2755	7545.8133	0.0000	1.0000
SYMIG	42	-3729.5122	7547.2390	0.0000	1.0000
SYMI	41	-3732.2596	7550.5333	0.0000	1.0000
K2PIG	38	-3735.7995	7551.0414	0.0000	1.0000
K2PI	37	-3738.3629	7553.9879	0.0000	1.0000
JC69G	36	-3775.6933	7626.4734	0.0000	1.0000
JC69IG	37	-3775.6613	7628.5848	0.0000	1.0000
F81	38	-3775.9966	7631.4356	0.0000	1.0000
JC69I	36	-3778.2837	7631.6544	0.0000	1.0000
SYM	40	-3789.4581	7662.7345	0.0000	1.0000
K2P	36	-3795.1265	7665.3399	0.0000	1.0000
JC69	35	-3832.8165	7738.5496	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3655.6057	7399.2113	0.7752	0.7752
GTRIG	45	-3655.9682	7401.9365	0.1985	0.9737
GTRI	44	-3659.2371	7406.4742	0.0205	0.9942
HKYG	40	-3664.7821	7409.5642	0.0044	0.9986
HKYIG	41	-3664.9688	7411.9376	0.0013	0.9999
HKYI	40	-3668.5654	7417.1307	0.0001	1.0000
F81IG	40	-3717.1837	7514.3674	0.0000	1.0000
F81G	39	-3718.5939	7515.1878	0.0000	1.0000
F81I	39	-3719.8426	7517.6853	0.0000	1.0000
GTR	43	-3717.9712	7521.9424	0.0000	1.0000
HKY	39	-3726.6913	7531.3825	0.0000	1.0000
SYMG	41	-3727.6312	7537.2624	0.0000	1.0000
K2PG	37	-3734.2755	7542.5511	0.0000	1.0000
SYMIG	42	-3729.5122	7543.0243	0.0000	1.0000
SYMI	41	-3732.2596	7546.5193	0.0000	1.0000
K2PIG	38	-3735.7995	7547.5989	0.0000	1.0000
K2PI	37	-3738.3629	7550.7257	0.0000	1.0000
JC69G	36	-3775.6933	7623.3865	0.0000	1.0000
JC69IG	37	-3775.6613	7625.3226	0.0000	1.0000
F81	38	-3775.9966	7627.9931	0.0000	1.0000
JC69I	36	-3778.2837	7628.5675	0.0000	1.0000
SYM	40	-3789.4581	7658.9161	0.0000	1.0000
K2P	36	-3795.1265	7662.2530	0.0000	1.0000
JC69	35	-3832.8165	7735.6329	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3664.7821	7601.6600	0.9408	0.9408
HKYIG	41	-3664.9688	7608.8358	0.0260	0.9668
HKYI	40	-3668.5654	7609.2265	0.0214	0.9882
GTRG	44	-3655.6057	7610.5167	0.0112	0.9994
GTRI	44	-3659.2371	7617.7795	0.0003	0.9997
GTRIG	45	-3655.9682	7618.0442	0.0003	1.0000
F81G	39	-3718.5939	7702.4812	0.0000	1.0000
F81I	39	-3719.8426	7704.9787	0.0000	1.0000
F81IG	40	-3717.1837	7706.4632	0.0000	1.0000
HKY	39	-3726.6913	7718.6759	0.0000	1.0000
K2PG	37	-3734.2755	7720.2397	0.0000	1.0000
K2PI	37	-3738.3629	7728.4143	0.0000	1.0000
GTR	43	-3717.9712	7728.4454	0.0000	1.0000
K2PIG	38	-3735.7995	7730.0899	0.0000	1.0000
SYMG	41	-3727.6312	7734.1606	0.0000	1.0000
SYMI	41	-3732.2596	7743.4175	0.0000	1.0000
SYMIG	42	-3729.5122	7744.7249	0.0000	1.0000
JC69G	36	-3775.6933	7796.2728	0.0000	1.0000
JC69I	36	-3778.2837	7801.4537	0.0000	1.0000
JC69IG	37	-3775.6613	7803.0112	0.0000	1.0000
F81	38	-3775.9966	7810.4841	0.0000	1.0000
K2P	36	-3795.1265	7835.1392	0.0000	1.0000
SYM	40	-3789.4581	7851.0119	0.0000	1.0000
JC69	35	-3832.8165	7903.7167	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/chrZ_13094.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_13094.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/chrZ_13094.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_13094.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/chrZ_13094.phylip = 1 - 900;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_13094.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

