
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:13 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/chr11_4777.phylip" (19 taxa, 498 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	-1876.7410	3840.6592	0.4108	0.4108
GTRG	44	-1872.2037	3841.1491	0.3216	0.7324
HKYIG	41	-1876.5182	3842.5890	0.1565	0.8890
GTRIG	45	-1872.1035	3843.3663	0.1061	0.9951
HKYI	40	-1881.5958	3850.3688	0.0032	0.9983
GTRI	44	-1877.4590	3851.6598	0.0017	1.0000
K2PG	37	-1894.2391	3868.5912	0.0000	1.0000
K2PIG	38	-1893.9956	3870.4487	0.0000	1.0000
SYMG	41	-1893.9429	3877.4384	0.0000	1.0000
K2PI	37	-1899.2061	3878.5252	0.0000	1.0000
SYMIG	42	-1893.8544	3879.6472	0.0000	1.0000
SYMI	41	-1897.8353	3885.2232	0.0000	1.0000
GTR	43	-1902.7406	3899.8161	0.0000	1.0000
HKY	39	-1907.7988	3900.4099	0.0000	1.0000
F81G	39	-1909.2599	3903.3321	0.0000	1.0000
F81IG	40	-1909.2006	3905.5784	0.0000	1.0000
F81I	39	-1913.2336	3911.2794	0.0000	1.0000
JC69G	36	-1922.5648	3922.9083	0.0000	1.0000
JC69IG	37	-1922.4940	3925.1009	0.0000	1.0000
K2P	36	-1925.8858	3929.5503	0.0000	1.0000
JC69I	36	-1926.4913	3930.7613	0.0000	1.0000
SYM	40	-1922.8957	3932.9686	0.0000	1.0000
F81	38	-1937.3551	3957.1677	0.0000	1.0000
JC69	35	-1951.0136	3977.4817	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1872.2037	3832.4074	0.4406	0.4406
HKYG	40	-1876.7410	3833.4820	0.2575	0.6981
GTRIG	45	-1872.1035	3834.2070	0.1792	0.8773
HKYIG	41	-1876.5182	3835.0364	0.1184	0.9957
GTRI	44	-1877.4590	3842.9181	0.0023	0.9980
HKYI	40	-1881.5958	3843.1915	0.0020	1.0000
K2PG	37	-1894.2391	3862.4781	0.0000	1.0000
K2PIG	38	-1893.9956	3863.9912	0.0000	1.0000
SYMG	41	-1893.9429	3869.8858	0.0000	1.0000
SYMIG	42	-1893.8544	3871.7088	0.0000	1.0000
K2PI	37	-1899.2061	3872.4122	0.0000	1.0000
SYMI	41	-1897.8353	3877.6706	0.0000	1.0000
GTR	43	-1902.7406	3891.4813	0.0000	1.0000
HKY	39	-1907.7988	3893.5977	0.0000	1.0000
F81G	39	-1909.2599	3896.5199	0.0000	1.0000
F81IG	40	-1909.2006	3898.4011	0.0000	1.0000
F81I	39	-1913.2336	3904.4672	0.0000	1.0000
JC69G	36	-1922.5648	3917.1295	0.0000	1.0000
JC69IG	37	-1922.4940	3918.9879	0.0000	1.0000
K2P	36	-1925.8858	3923.7716	0.0000	1.0000
JC69I	36	-1926.4913	3924.9825	0.0000	1.0000
SYM	40	-1922.8957	3925.7913	0.0000	1.0000
F81	38	-1937.3551	3950.7102	0.0000	1.0000
JC69	35	-1951.0136	3972.0272	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1876.7410	4001.9060	0.9394	0.9394
HKYIG	41	-1876.5182	4007.6710	0.0526	0.9920
HKYI	40	-1881.5958	4011.6155	0.0073	0.9993
GTRG	44	-1872.2037	4017.6738	0.0004	0.9997
K2PG	37	-1894.2391	4018.2703	0.0003	1.0000
GTRIG	45	-1872.1035	4023.6840	0.0000	1.0000
K2PIG	38	-1893.9956	4023.9940	0.0000	1.0000
GTRI	44	-1877.4590	4028.1845	0.0000	1.0000
K2PI	37	-1899.2061	4028.2044	0.0000	1.0000
SYMG	41	-1893.9429	4042.5204	0.0000	1.0000
SYMIG	42	-1893.8544	4048.5540	0.0000	1.0000
SYMI	41	-1897.8353	4050.3052	0.0000	1.0000
HKY	39	-1907.7988	4057.8111	0.0000	1.0000
F81G	39	-1909.2599	4060.7333	0.0000	1.0000
F81IG	40	-1909.2006	4066.8251	0.0000	1.0000
F81I	39	-1913.2336	4068.6806	0.0000	1.0000
JC69G	36	-1922.5648	4068.7111	0.0000	1.0000
GTR	43	-1902.7406	4072.5371	0.0000	1.0000
JC69IG	37	-1922.4940	4074.7801	0.0000	1.0000
K2P	36	-1925.8858	4075.3532	0.0000	1.0000
JC69I	36	-1926.4913	4076.5641	0.0000	1.0000
SYM	40	-1922.8957	4094.2153	0.0000	1.0000
F81	38	-1937.3551	4110.7130	0.0000	1.0000
JC69	35	-1951.0136	4119.3982	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/chr11_4777.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4777.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/chr11_4777.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4777.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/chr11_4777.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4777.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

