
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:45 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_25816.phylip" (19 taxa, 491 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	-1817.5974	3732.0736	0.4951	0.4951
HKYG	40	-1822.6845	3732.6580	0.3696	0.8647
HKYIG	41	-1823.4278	3736.5260	0.0534	0.9182
HKYI	40	-1824.7322	3736.7533	0.0477	0.9659
GTRIG	45	-1819.6298	3738.5630	0.0193	0.9852
GTRI	44	-1821.1047	3739.0883	0.0148	1.0000
GTR	43	-1836.9903	3768.4458	0.0000	1.0000
HKY	39	-1844.3434	3773.6047	0.0000	1.0000
SYMG	41	-1844.4617	3778.5938	0.0000	1.0000
K2PG	37	-1850.1426	3780.4927	0.0000	1.0000
K2PI	37	-1852.0742	3784.3559	0.0000	1.0000
K2PIG	38	-1850.9643	3784.4861	0.0000	1.0000
SYMIG	42	-1846.5948	3785.2520	0.0000	1.0000
SYMI	41	-1847.8402	3785.3509	0.0000	1.0000
F81G	39	-1861.5610	3808.0399	0.0000	1.0000
F81I	39	-1864.1601	3813.2382	0.0000	1.0000
F81IG	40	-1862.9992	3813.2873	0.0000	1.0000
SYM	40	-1864.7981	3816.8850	0.0000	1.0000
K2P	36	-1872.1000	3822.0679	0.0000	1.0000
JC69G	36	-1882.7735	3843.4149	0.0000	1.0000
F81	38	-1881.5232	3845.6040	0.0000	1.0000
JC69I	36	-1885.8563	3849.5805	0.0000	1.0000
JC69IG	37	-1884.6982	3849.6040	0.0000	1.0000
JC69	35	-1903.0948	3881.7280	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1817.5974	3723.1947	0.6588	0.6588
HKYG	40	-1822.6845	3725.3691	0.2221	0.8810
HKYIG	41	-1823.4278	3728.8556	0.0389	0.9198
GTRIG	45	-1819.6298	3729.2596	0.0318	0.9516
HKYI	40	-1824.7322	3729.4645	0.0287	0.9803
GTRI	44	-1821.1047	3730.2094	0.0197	1.0000
GTR	43	-1836.9903	3759.9805	0.0000	1.0000
HKY	39	-1844.3434	3766.6868	0.0000	1.0000
SYMG	41	-1844.4617	3770.9235	0.0000	1.0000
K2PG	37	-1850.1426	3774.2852	0.0000	1.0000
SYMIG	42	-1846.5948	3777.1895	0.0000	1.0000
SYMI	41	-1847.8402	3777.6805	0.0000	1.0000
K2PIG	38	-1850.9643	3777.9286	0.0000	1.0000
K2PI	37	-1852.0742	3778.1484	0.0000	1.0000
F81G	39	-1861.5610	3801.1220	0.0000	1.0000
F81IG	40	-1862.9992	3805.9984	0.0000	1.0000
F81I	39	-1864.1601	3806.3202	0.0000	1.0000
SYM	40	-1864.7981	3809.5961	0.0000	1.0000
K2P	36	-1872.1000	3816.2001	0.0000	1.0000
JC69G	36	-1882.7735	3837.5470	0.0000	1.0000
F81	38	-1881.5232	3839.0464	0.0000	1.0000
JC69IG	37	-1884.6982	3843.3965	0.0000	1.0000
JC69I	36	-1885.8563	3843.7127	0.0000	1.0000
JC69	35	-1903.0948	3876.1896	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1822.6845	3893.2268	0.8687	0.8687
HKYI	40	-1824.7322	3897.3222	0.1121	0.9808
HKYIG	41	-1823.4278	3900.9098	0.0186	0.9994
GTRG	44	-1817.5974	3907.8382	0.0006	1.0000
GTRI	44	-1821.1047	3914.8530	0.0000	1.0000
GTRIG	45	-1819.6298	3918.0996	0.0000	1.0000
K2PG	37	-1850.1426	3929.5536	0.0000	1.0000
HKY	39	-1844.3434	3930.3481	0.0000	1.0000
K2PI	37	-1852.0742	3933.4169	0.0000	1.0000
K2PIG	38	-1850.9643	3937.3934	0.0000	1.0000
GTR	43	-1836.9903	3940.4276	0.0000	1.0000
SYMG	41	-1844.4617	3942.9777	0.0000	1.0000
SYMI	41	-1847.8402	3949.7347	0.0000	1.0000
SYMIG	42	-1846.5948	3953.4402	0.0000	1.0000
F81G	39	-1861.5610	3964.7833	0.0000	1.0000
K2P	36	-1872.1000	3967.2721	0.0000	1.0000
F81I	39	-1864.1601	3969.9815	0.0000	1.0000
F81IG	40	-1862.9992	3973.8562	0.0000	1.0000
SYM	40	-1864.7981	3977.4539	0.0000	1.0000
JC69G	36	-1882.7735	3988.6190	0.0000	1.0000
JC69I	36	-1885.8563	3994.7847	0.0000	1.0000
F81	38	-1881.5232	3998.5113	0.0000	1.0000
JC69IG	37	-1884.6982	3998.6649	0.0000	1.0000
JC69	35	-1903.0948	4023.0651	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_25816.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25816.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_25816.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25816.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_25816.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25816.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

