
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:05 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_32234.phylip" (19 taxa, 451 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	-1744.0811	3576.1622	0.3002	0.3002
GTRG	44	-1739.5090	3576.7717	0.2213	0.5215
HKYI	40	-1744.7216	3577.4433	0.1582	0.6797
GTRI	44	-1739.9620	3577.6777	0.1407	0.8204
HKYIG	41	-1743.9615	3578.3436	0.1009	0.9212
GTRIG	45	-1739.3079	3578.8380	0.0788	1.0000
K2PG	37	-1759.8373	3600.4834	0.0000	1.0000
SYMG	41	-1757.9911	3606.4027	0.0000	1.0000
K2PIG	38	-1761.6715	3606.5372	0.0000	1.0000
K2PI	37	-1763.6882	3608.1852	0.0000	1.0000
SYMIG	42	-1759.8039	3612.4608	0.0000	1.0000
SYMI	41	-1761.7900	3614.0005	0.0000	1.0000
HKY	39	-1767.7539	3621.0991	0.0000	1.0000
GTR	43	-1763.7552	3622.8076	0.0000	1.0000
K2P	36	-1783.2063	3644.8474	0.0000	1.0000
SYM	40	-1781.3977	3650.7954	0.0000	1.0000
F81G	39	-1811.5676	3708.7264	0.0000	1.0000
F81I	39	-1812.5738	3710.7388	0.0000	1.0000
F81IG	40	-1811.5521	3711.1043	0.0000	1.0000
JC69G	36	-1822.2364	3722.9076	0.0000	1.0000
JC69IG	37	-1824.4667	3729.7421	0.0000	1.0000
JC69I	36	-1826.1479	3730.7305	0.0000	1.0000
F81	38	-1833.5832	3750.3606	0.0000	1.0000
JC69	35	-1844.4296	3764.9315	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1739.5090	3567.0180	0.3143	0.3143
GTRI	44	-1739.9620	3567.9240	0.1998	0.5142
HKYG	40	-1744.0811	3568.1622	0.1774	0.6916
GTRIG	45	-1739.3079	3568.6158	0.1414	0.8330
HKYI	40	-1744.7216	3569.4433	0.0935	0.9265
HKYIG	41	-1743.9615	3569.9230	0.0735	1.0000
K2PG	37	-1759.8373	3593.6747	0.0000	1.0000
SYMG	41	-1757.9911	3597.9822	0.0000	1.0000
K2PIG	38	-1761.6715	3599.3430	0.0000	1.0000
K2PI	37	-1763.6882	3601.3765	0.0000	1.0000
SYMIG	42	-1759.8039	3603.6079	0.0000	1.0000
SYMI	41	-1761.7900	3605.5800	0.0000	1.0000
HKY	39	-1767.7539	3613.5078	0.0000	1.0000
GTR	43	-1763.7552	3613.5103	0.0000	1.0000
K2P	36	-1783.2063	3638.4127	0.0000	1.0000
SYM	40	-1781.3977	3642.7954	0.0000	1.0000
F81G	39	-1811.5676	3701.1351	0.0000	1.0000
F81IG	40	-1811.5521	3703.1043	0.0000	1.0000
F81I	39	-1812.5738	3703.1476	0.0000	1.0000
JC69G	36	-1822.2364	3716.4728	0.0000	1.0000
JC69IG	37	-1824.4667	3722.9334	0.0000	1.0000
JC69I	36	-1826.1479	3724.2957	0.0000	1.0000
F81	38	-1833.5832	3743.1664	0.0000	1.0000
JC69	35	-1844.4296	3758.8592	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1744.0811	3732.6209	0.6320	0.6320
HKYI	40	-1744.7216	3733.9020	0.3331	0.9651
HKYIG	41	-1743.9615	3738.4932	0.0335	0.9986
K2PG	37	-1759.8373	3745.7990	0.0009	0.9995
GTRG	44	-1739.5090	3747.9225	0.0003	0.9998
GTRI	44	-1739.9620	3748.8286	0.0002	1.0000
K2PI	37	-1763.6882	3753.5008	0.0000	1.0000
GTRIG	45	-1739.3079	3753.6318	0.0000	1.0000
K2PIG	38	-1761.6715	3755.5787	0.0000	1.0000
SYMG	41	-1757.9911	3766.5524	0.0000	1.0000
HKY	39	-1767.7539	3773.8550	0.0000	1.0000
SYMI	41	-1761.7900	3774.1502	0.0000	1.0000
SYMIG	42	-1759.8039	3776.2895	0.0000	1.0000
K2P	36	-1783.2063	3786.4255	0.0000	1.0000
GTR	43	-1763.7552	3790.3034	0.0000	1.0000
SYM	40	-1781.3977	3807.2541	0.0000	1.0000
F81G	39	-1811.5676	3861.4823	0.0000	1.0000
F81I	39	-1812.5738	3863.4948	0.0000	1.0000
JC69G	36	-1822.2364	3864.4856	0.0000	1.0000
F81IG	40	-1811.5521	3867.5630	0.0000	1.0000
JC69I	36	-1826.1479	3872.3085	0.0000	1.0000
JC69IG	37	-1824.4667	3875.0577	0.0000	1.0000
F81	38	-1833.5832	3899.4021	0.0000	1.0000
JC69	35	-1844.4296	3902.7606	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/chr1_32234.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32234.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/chr1_32234.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32234.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/chr1_32234.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32234.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

