
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:03 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/chr2_8026.phylip" (19 taxa, 894 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	-2667.4760	5427.6163	0.5524	0.5524
GTRIG	45	-2667.3996	5429.6814	0.1967	0.7491
GTRI	44	-2668.5359	5429.7360	0.1914	0.9405
HKYG	40	-2674.6801	5433.2055	0.0338	0.9743
HKYI	40	-2675.6370	5435.1193	0.0130	0.9873
HKYIG	41	-2674.5588	5435.1598	0.0127	1.0000
F81G	39	-2692.1166	5465.8866	0.0000	1.0000
SYMG	41	-2690.3309	5466.7041	0.0000	1.0000
F81I	39	-2692.9117	5467.4767	0.0000	1.0000
F81IG	40	-2692.0745	5467.9943	0.0000	1.0000
SYMIG	42	-2690.1111	5468.4666	0.0000	1.0000
SYMI	41	-2691.7603	5469.5628	0.0000	1.0000
K2PG	37	-2699.0651	5475.4153	0.0000	1.0000
K2PIG	38	-2698.9107	5477.2881	0.0000	1.0000
K2PI	37	-2700.1455	5477.5761	0.0000	1.0000
JC69G	36	-2716.7159	5508.5404	0.0000	1.0000
JC69IG	37	-2716.6115	5510.5081	0.0000	1.0000
JC69I	36	-2717.7115	5510.5314	0.0000	1.0000
GTR	43	-2726.5296	5543.5109	0.0000	1.0000
HKY	39	-2734.9891	5551.6317	0.0000	1.0000
SYM	40	-2746.4838	5576.8129	0.0000	1.0000
F81	38	-2750.8728	5581.2122	0.0000	1.0000
K2P	36	-2757.0586	5589.2257	0.0000	1.0000
JC69	35	-2773.5511	5620.0392	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2667.4760	5422.9520	0.5505	0.5505
GTRIG	45	-2667.3996	5424.7993	0.2186	0.7690
GTRI	44	-2668.5359	5425.0717	0.1907	0.9598
HKYG	40	-2674.6801	5429.3602	0.0223	0.9821
HKYIG	41	-2674.5588	5431.1175	0.0093	0.9914
HKYI	40	-2675.6370	5431.2740	0.0086	1.0000
F81G	39	-2692.1166	5462.2332	0.0000	1.0000
SYMG	41	-2690.3309	5462.6619	0.0000	1.0000
F81I	39	-2692.9117	5463.8233	0.0000	1.0000
F81IG	40	-2692.0745	5464.1491	0.0000	1.0000
SYMIG	42	-2690.1111	5464.2222	0.0000	1.0000
SYMI	41	-2691.7603	5465.5205	0.0000	1.0000
K2PG	37	-2699.0651	5472.1303	0.0000	1.0000
K2PIG	38	-2698.9107	5473.8215	0.0000	1.0000
K2PI	37	-2700.1455	5474.2911	0.0000	1.0000
JC69G	36	-2716.7159	5505.4319	0.0000	1.0000
JC69IG	37	-2716.6115	5507.2231	0.0000	1.0000
JC69I	36	-2717.7115	5507.4229	0.0000	1.0000
GTR	43	-2726.5296	5539.0591	0.0000	1.0000
HKY	39	-2734.9891	5547.9783	0.0000	1.0000
SYM	40	-2746.4838	5572.9676	0.0000	1.0000
F81	38	-2750.8728	5577.7455	0.0000	1.0000
K2P	36	-2757.0586	5586.1172	0.0000	1.0000
JC69	35	-2773.5511	5617.1022	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2674.6801	5621.1885	0.7022	0.7022
HKYI	40	-2675.6370	5623.1023	0.2697	0.9719
HKYIG	41	-2674.5588	5627.7415	0.0265	0.9984
GTRG	44	-2667.4760	5633.9631	0.0012	0.9995
GTRI	44	-2668.5359	5636.0828	0.0004	1.0000
GTRIG	45	-2667.3996	5640.6061	0.0000	1.0000
F81G	39	-2692.1166	5649.2658	0.0000	1.0000
K2PG	37	-2699.0651	5649.5714	0.0000	1.0000
F81I	39	-2692.9117	5650.8559	0.0000	1.0000
K2PI	37	-2700.1455	5651.7322	0.0000	1.0000
F81IG	40	-2692.0745	5655.9773	0.0000	1.0000
K2PIG	38	-2698.9107	5656.0583	0.0000	1.0000
SYMG	41	-2690.3309	5659.2858	0.0000	1.0000
SYMI	41	-2691.7603	5662.1445	0.0000	1.0000
SYMIG	42	-2690.1111	5665.6418	0.0000	1.0000
JC69G	36	-2716.7159	5678.0773	0.0000	1.0000
JC69I	36	-2717.7115	5680.0683	0.0000	1.0000
JC69IG	37	-2716.6115	5684.6642	0.0000	1.0000
HKY	39	-2734.9891	5735.0108	0.0000	1.0000
GTR	43	-2726.5296	5745.2744	0.0000	1.0000
K2P	36	-2757.0586	5758.7626	0.0000	1.0000
F81	38	-2750.8728	5759.9823	0.0000	1.0000
SYM	40	-2746.4838	5764.7959	0.0000	1.0000
JC69	35	-2773.5511	5784.9519	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/chr2_8026.phylip = 1 - 894;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8026.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/chr2_8026.phylip = 1 - 894;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8026.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/chr2_8026.phylip = 1 - 894;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8026.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

