
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:14 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/chr13_714.phylip" (19 taxa, 574 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1714.9166	3515.9870	0.3264	0.3264
GTRG	44	-1710.4119	3516.3097	0.2778	0.6042
HKYIG	41	-1714.7352	3517.9440	0.1227	0.7268
GTRIG	45	-1710.1711	3518.1831	0.1089	0.8357
HKYI	40	-1716.0461	3518.2460	0.1055	0.9412
GTRI	44	-1711.9645	3519.4148	0.0588	1.0000
HKY	39	-1742.0127	3567.8681	0.0000	1.0000
GTR	43	-1737.9704	3569.0805	0.0000	1.0000
F81G	39	-1746.1279	3576.0986	0.0000	1.0000
F81I	39	-1746.9155	3577.6738	0.0000	1.0000
F81IG	40	-1746.0613	3578.2765	0.0000	1.0000
K2PG	37	-1765.2126	3609.6715	0.0000	1.0000
K2PI	37	-1765.8997	3611.0456	0.0000	1.0000
K2PIG	38	-1765.0463	3611.6327	0.0000	1.0000
SYMG	41	-1764.0880	3616.6496	0.0000	1.0000
SYMI	41	-1764.7845	3618.0426	0.0000	1.0000
SYMIG	42	-1763.9414	3618.6850	0.0000	1.0000
F81	38	-1772.4643	3626.4687	0.0000	1.0000
JC69G	36	-1788.8229	3654.6068	0.0000	1.0000
JC69I	36	-1789.4572	3655.8753	0.0000	1.0000
JC69IG	37	-1788.7739	3656.7940	0.0000	1.0000
K2P	36	-1793.3920	3663.7450	0.0000	1.0000
SYM	40	-1791.7332	3669.6203	0.0000	1.0000
JC69	35	-1816.1466	3706.9773	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1710.4119	3508.8239	0.3643	0.3643
HKYG	40	-1714.9166	3509.8332	0.2199	0.5843
GTRIG	45	-1710.1711	3510.3422	0.1705	0.7548
HKYIG	41	-1714.7352	3511.4703	0.0970	0.8518
GTRI	44	-1711.9645	3511.9290	0.0771	0.9289
HKYI	40	-1716.0461	3512.0921	0.0711	1.0000
GTR	43	-1737.9704	3561.9408	0.0000	1.0000
HKY	39	-1742.0127	3562.0254	0.0000	1.0000
F81G	39	-1746.1279	3570.2559	0.0000	1.0000
F81I	39	-1746.9155	3571.8311	0.0000	1.0000
F81IG	40	-1746.0613	3572.1227	0.0000	1.0000
K2PG	37	-1765.2126	3604.4253	0.0000	1.0000
K2PI	37	-1765.8997	3605.7993	0.0000	1.0000
K2PIG	38	-1765.0463	3606.0926	0.0000	1.0000
SYMG	41	-1764.0880	3610.1759	0.0000	1.0000
SYMI	41	-1764.7845	3611.5690	0.0000	1.0000
SYMIG	42	-1763.9414	3611.8828	0.0000	1.0000
F81	38	-1772.4643	3620.9285	0.0000	1.0000
JC69G	36	-1788.8229	3649.6459	0.0000	1.0000
JC69I	36	-1789.4572	3650.9144	0.0000	1.0000
JC69IG	37	-1788.7739	3651.5478	0.0000	1.0000
K2P	36	-1793.3920	3658.7841	0.0000	1.0000
SYM	40	-1791.7332	3663.4665	0.0000	1.0000
JC69	35	-1816.1466	3702.2933	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1714.9166	3683.9383	0.7280	0.7280
HKYI	40	-1716.0461	3686.1973	0.2353	0.9633
HKYIG	41	-1714.7352	3689.9281	0.0364	0.9997
GTRG	44	-1710.4119	3700.3396	0.0002	0.9999
GTRI	44	-1711.9645	3703.4447	0.0000	1.0000
GTRIG	45	-1710.1711	3706.2105	0.0000	1.0000
HKY	39	-1742.0127	3731.7780	0.0000	1.0000
F81G	39	-1746.1279	3740.0084	0.0000	1.0000
F81I	39	-1746.9155	3741.5836	0.0000	1.0000
F81IG	40	-1746.0613	3746.2279	0.0000	1.0000
GTR	43	-1737.9704	3749.1039	0.0000	1.0000
K2PG	37	-1765.2126	3765.4726	0.0000	1.0000
K2PI	37	-1765.8997	3766.8466	0.0000	1.0000
K2PIG	38	-1765.0463	3771.4925	0.0000	1.0000
F81	38	-1772.4643	3786.3285	0.0000	1.0000
SYMG	41	-1764.0880	3788.6337	0.0000	1.0000
SYMI	41	-1764.7845	3790.0268	0.0000	1.0000
SYMIG	42	-1763.9414	3794.6932	0.0000	1.0000
JC69G	36	-1788.8229	3806.3406	0.0000	1.0000
JC69I	36	-1789.4572	3807.6091	0.0000	1.0000
JC69IG	37	-1788.7739	3812.5951	0.0000	1.0000
K2P	36	-1793.3920	3815.4787	0.0000	1.0000
SYM	40	-1791.7332	3837.5717	0.0000	1.0000
JC69	35	-1816.1466	3854.6353	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/chr13_714.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_714.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_714.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_714.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;


[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/chr13_714.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_714.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

