
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:37 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/chr7_10445.phylip" (19 taxa, 610 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	-1826.4595	3747.9278	0.5196	0.5196
GTRIG	45	-1825.8773	3749.0950	0.2899	0.8095
GTRI	44	-1828.4440	3751.8968	0.0714	0.8809
HKYG	40	-1833.1077	3751.9799	0.0685	0.9494
HKYIG	41	-1832.5149	3753.0932	0.0393	0.9887
HKYI	40	-1834.9067	3755.5779	0.0113	1.0000
K2PG	37	-1854.4833	3787.8826	0.0000	1.0000
SYMG	41	-1850.3982	3788.8599	0.0000	1.0000
K2PIG	38	-1854.0411	3789.2732	0.0000	1.0000
SYMIG	42	-1849.9884	3790.3472	0.0000	1.0000
K2PI	37	-1856.0192	3790.9544	0.0000	1.0000
SYMI	41	-1852.0788	3792.2210	0.0000	1.0000
GTR	43	-1853.2494	3799.1843	0.0000	1.0000
HKY	39	-1860.9198	3805.3133	0.0000	1.0000
SYM	40	-1876.3177	3838.3999	0.0000	1.0000
K2P	36	-1882.2467	3841.1427	0.0000	1.0000
F81G	39	-1883.5985	3850.6707	0.0000	1.0000
F81IG	40	-1883.2218	3852.2080	0.0000	1.0000
F81I	39	-1885.1545	3853.7827	0.0000	1.0000
JC69G	36	-1900.8245	3878.2982	0.0000	1.0000
JC69IG	37	-1900.4707	3879.8576	0.0000	1.0000
JC69I	36	-1902.3135	3881.2763	0.0000	1.0000
F81	38	-1910.4285	3902.0479	0.0000	1.0000
JC69	35	-1927.7020	3929.7942	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1826.4595	3740.9190	0.5193	0.5193
GTRIG	45	-1825.8773	3741.7546	0.3420	0.8613
GTRI	44	-1828.4440	3744.8879	0.0714	0.9327
HKYG	40	-1833.1077	3746.2154	0.0368	0.9695
HKYIG	41	-1832.5149	3747.0298	0.0245	0.9939
HKYI	40	-1834.9067	3749.8134	0.0061	1.0000
SYMG	41	-1850.3982	3782.7965	0.0000	1.0000
K2PG	37	-1854.4833	3782.9666	0.0000	1.0000
SYMIG	42	-1849.9884	3783.9769	0.0000	1.0000
K2PIG	38	-1854.0411	3784.0823	0.0000	1.0000
K2PI	37	-1856.0192	3786.0384	0.0000	1.0000
SYMI	41	-1852.0788	3786.1576	0.0000	1.0000
GTR	43	-1853.2494	3792.4988	0.0000	1.0000
HKY	39	-1860.9198	3799.8396	0.0000	1.0000
SYM	40	-1876.3177	3832.6354	0.0000	1.0000
K2P	36	-1882.2467	3836.4934	0.0000	1.0000
F81G	39	-1883.5985	3845.1970	0.0000	1.0000
F81IG	40	-1883.2218	3846.4435	0.0000	1.0000
F81I	39	-1885.1545	3848.3091	0.0000	1.0000
JC69G	36	-1900.8245	3873.6489	0.0000	1.0000
JC69IG	37	-1900.4707	3874.9415	0.0000	1.0000
JC69I	36	-1902.3135	3876.6271	0.0000	1.0000
F81	38	-1910.4285	3896.8570	0.0000	1.0000
JC69	35	-1927.7020	3925.4039	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1833.1077	3922.7538	0.8056	0.8056
HKYI	40	-1834.9067	3926.3517	0.1333	0.9390
HKYIG	41	-1832.5149	3927.9816	0.0590	0.9980
GTRG	44	-1826.4595	3935.1112	0.0017	0.9996
GTRI	44	-1828.4440	3939.0801	0.0002	0.9999
GTRIG	45	-1825.8773	3940.3603	0.0001	1.0000
K2PG	37	-1854.4833	3946.2645	0.0000	1.0000
K2PI	37	-1856.0192	3949.3363	0.0000	1.0000
K2PIG	38	-1854.0411	3951.7937	0.0000	1.0000
SYMG	41	-1850.3982	3963.7483	0.0000	1.0000
SYMI	41	-1852.0788	3967.1095	0.0000	1.0000
SYMIG	42	-1849.9884	3969.3421	0.0000	1.0000
HKY	39	-1860.9198	3971.9645	0.0000	1.0000
GTR	43	-1853.2494	3982.2775	0.0000	1.0000
K2P	36	-1882.2467	3995.3780	0.0000	1.0000
SYM	40	-1876.3177	4009.1738	0.0000	1.0000
F81G	39	-1883.5985	4017.3219	0.0000	1.0000
F81I	39	-1885.1545	4020.4340	0.0000	1.0000
F81IG	40	-1883.2218	4022.9819	0.0000	1.0000
JC69G	36	-1900.8245	4032.5335	0.0000	1.0000
JC69I	36	-1902.3135	4035.5116	0.0000	1.0000
JC69IG	37	-1900.4707	4038.2395	0.0000	1.0000
F81	38	-1910.4285	4064.5685	0.0000	1.0000
JC69	35	-1927.7020	4079.8750	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/chr7_10445.phylip = 1 - 610;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10445.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/chr7_10445.phylip = 1 - 610;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10445.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/chr7_10445.phylip = 1 - 610;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10445.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

