
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:28 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/chr9_3566.phylip" (19 taxa, 547 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	-1760.7444	3607.9711	0.3668	0.3668
GTRG	44	-1756.1858	3608.2601	0.3174	0.6842
HKYIG	41	-1760.5914	3610.0027	0.1328	0.8170
GTRIG	45	-1756.0508	3610.3651	0.1108	0.9278
HKYI	40	-1762.8913	3612.2648	0.0429	0.9706
GTRI	44	-1758.5658	3613.0200	0.0294	1.0000
K2PG	37	-1779.2665	3638.0575	0.0000	1.0000
SYMG	41	-1775.3327	3639.4852	0.0000	1.0000
GTR	43	-1773.1845	3639.8919	0.0000	1.0000
K2PIG	38	-1779.1080	3640.0507	0.0000	1.0000
HKY	39	-1778.4020	3640.9578	0.0000	1.0000
SYMIG	42	-1775.2037	3641.5740	0.0000	1.0000
K2PI	37	-1781.3186	3642.1618	0.0000	1.0000
SYMI	41	-1777.4944	3643.8087	0.0000	1.0000
F81G	39	-1787.4916	3659.1370	0.0000	1.0000
F81IG	40	-1787.3918	3661.2658	0.0000	1.0000
F81I	39	-1789.3145	3662.7827	0.0000	1.0000
SYM	40	-1792.8501	3672.1823	0.0000	1.0000
K2P	36	-1797.4930	3672.2094	0.0000	1.0000
JC69G	36	-1804.4893	3686.2022	0.0000	1.0000
JC69IG	37	-1804.3990	3688.3225	0.0000	1.0000
JC69I	36	-1806.3006	3689.8247	0.0000	1.0000
F81	38	-1808.2231	3698.2808	0.0000	1.0000
JC69	35	-1825.1264	3725.1843	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1756.1858	3600.3716	0.4171	0.4171
HKYG	40	-1760.7444	3601.4889	0.2386	0.6556
GTRIG	45	-1756.0508	3602.1016	0.1756	0.8312
HKYIG	41	-1760.5914	3603.1829	0.1023	0.9335
GTRI	44	-1758.5658	3605.1316	0.0386	0.9721
HKYI	40	-1762.8913	3605.7826	0.0279	1.0000
GTR	43	-1773.1845	3632.3690	0.0000	1.0000
K2PG	37	-1779.2665	3632.5330	0.0000	1.0000
SYMG	41	-1775.3327	3632.6654	0.0000	1.0000
K2PIG	38	-1779.1080	3634.2161	0.0000	1.0000
SYMIG	42	-1775.2037	3634.4073	0.0000	1.0000
HKY	39	-1778.4020	3634.8040	0.0000	1.0000
K2PI	37	-1781.3186	3636.6373	0.0000	1.0000
SYMI	41	-1777.4944	3636.9889	0.0000	1.0000
F81G	39	-1787.4916	3652.9831	0.0000	1.0000
F81IG	40	-1787.3918	3654.7836	0.0000	1.0000
F81I	39	-1789.3145	3656.6289	0.0000	1.0000
SYM	40	-1792.8501	3665.7001	0.0000	1.0000
K2P	36	-1797.4930	3666.9859	0.0000	1.0000
JC69G	36	-1804.4893	3680.9787	0.0000	1.0000
JC69IG	37	-1804.3990	3682.7980	0.0000	1.0000
JC69I	36	-1806.3006	3684.6012	0.0000	1.0000
F81	38	-1808.2231	3692.4461	0.0000	1.0000
JC69	35	-1825.1264	3720.2528	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1760.7444	3773.6669	0.8568	0.8568
HKYI	40	-1762.8913	3777.9605	0.1001	0.9569
HKYIG	41	-1760.5914	3779.6653	0.0427	0.9996
GTRG	44	-1756.1858	3789.7674	0.0003	0.9998
K2PG	37	-1779.2665	3791.7976	0.0001	0.9999
GTRI	44	-1758.5658	3794.5273	0.0000	1.0000
GTRIG	45	-1756.0508	3795.8018	0.0000	1.0000
K2PI	37	-1781.3186	3795.9019	0.0000	1.0000
K2PIG	38	-1779.1080	3797.7851	0.0000	1.0000
HKY	39	-1778.4020	3802.6775	0.0000	1.0000
SYMG	41	-1775.3327	3809.1478	0.0000	1.0000
SYMI	41	-1777.4944	3813.4713	0.0000	1.0000
SYMIG	42	-1775.2037	3815.1942	0.0000	1.0000
GTR	43	-1773.1845	3817.4603	0.0000	1.0000
F81G	39	-1787.4916	3820.8566	0.0000	1.0000
K2P	36	-1797.4930	3821.9461	0.0000	1.0000
F81I	39	-1789.3145	3824.5024	0.0000	1.0000
F81IG	40	-1787.3918	3826.9615	0.0000	1.0000
JC69G	36	-1804.4893	3835.9388	0.0000	1.0000
SYM	40	-1792.8501	3837.8781	0.0000	1.0000
JC69I	36	-1806.3006	3839.5613	0.0000	1.0000
JC69IG	37	-1804.3990	3842.0626	0.0000	1.0000
F81	38	-1808.2231	3856.0152	0.0000	1.0000
JC69	35	-1825.1264	3870.9085	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/chr9_3566.phylip = 1 - 547;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3566.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/chr9_3566.phylip = 1 - 547;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3566.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/chr9_3566.phylip = 1 - 547;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3566.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

