
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:02 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_3428.phylip" (19 taxa, 622 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	-1809.8129	3714.4889	0.6040	0.6040
GTRIG	45	-1809.1485	3715.4846	0.3671	0.9712
GTRI	44	-1812.9355	3720.7340	0.0266	0.9978
HKYG	40	-1820.4693	3726.5840	0.0014	0.9992
HKYIG	41	-1820.0033	3727.9446	0.0007	0.9999
HKYI	40	-1823.3478	3732.3410	0.0001	1.0000
GTR	43	-1832.0885	3756.7237	0.0000	1.0000
HKY	39	-1839.8696	3763.1000	0.0000	1.0000
K2PG	37	-1843.3791	3765.5732	0.0000	1.0000
K2PIG	38	-1843.0230	3767.1300	0.0000	1.0000
SYMG	41	-1840.0923	3768.1226	0.0000	1.0000
SYMIG	42	-1839.7316	3769.7016	0.0000	1.0000
K2PI	37	-1846.2465	3771.3080	0.0000	1.0000
SYMI	41	-1842.8755	3773.6890	0.0000	1.0000
F81G	39	-1846.9444	3777.2495	0.0000	1.0000
F81IG	40	-1846.6215	3778.8884	0.0000	1.0000
F81I	39	-1849.6343	3782.6295	0.0000	1.0000
K2P	36	-1861.6279	3799.8095	0.0000	1.0000
SYM	40	-1858.4270	3802.4994	0.0000	1.0000
JC69G	36	-1865.3137	3807.1812	0.0000	1.0000
JC69IG	37	-1865.0290	3808.8731	0.0000	1.0000
F81	38	-1865.1417	3811.3674	0.0000	1.0000
JC69I	36	-1868.0103	3812.5743	0.0000	1.0000
JC69	35	-1883.0760	3840.4524	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1809.8129	3707.6258	0.5678	0.5678
GTRIG	45	-1809.1485	3708.2971	0.4059	0.9738
GTRI	44	-1812.9355	3713.8709	0.0250	0.9988
HKYG	40	-1820.4693	3720.9386	0.0007	0.9995
HKYIG	41	-1820.0033	3722.0066	0.0004	1.0000
HKYI	40	-1823.3478	3726.6956	0.0000	1.0000
GTR	43	-1832.0885	3750.1770	0.0000	1.0000
HKY	39	-1839.8696	3757.7391	0.0000	1.0000
K2PG	37	-1843.3791	3760.7582	0.0000	1.0000
K2PIG	38	-1843.0230	3762.0460	0.0000	1.0000
SYMG	41	-1840.0923	3762.1847	0.0000	1.0000
SYMIG	42	-1839.7316	3763.4632	0.0000	1.0000
K2PI	37	-1846.2465	3766.4930	0.0000	1.0000
SYMI	41	-1842.8755	3767.7511	0.0000	1.0000
F81G	39	-1846.9444	3771.8887	0.0000	1.0000
F81IG	40	-1846.6215	3773.2430	0.0000	1.0000
F81I	39	-1849.6343	3777.2686	0.0000	1.0000
K2P	36	-1861.6279	3795.2557	0.0000	1.0000
SYM	40	-1858.4270	3796.8540	0.0000	1.0000
JC69G	36	-1865.3137	3802.6274	0.0000	1.0000
JC69IG	37	-1865.0290	3804.0580	0.0000	1.0000
F81	38	-1865.1417	3806.2833	0.0000	1.0000
JC69I	36	-1868.0103	3808.0205	0.0000	1.0000
JC69	35	-1883.0760	3836.1521	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1820.4693	3898.2562	0.8043	0.8043
GTRG	44	-1809.8129	3902.6752	0.0883	0.8926
HKYIG	41	-1820.0033	3903.7572	0.0514	0.9440
HKYI	40	-1823.3478	3904.0132	0.0452	0.9892
GTRIG	45	-1809.1485	3907.7794	0.0069	0.9961
GTRI	44	-1812.9355	3908.9203	0.0039	1.0000
K2PG	37	-1843.3791	3924.7770	0.0000	1.0000
K2PIG	38	-1843.0230	3930.4977	0.0000	1.0000
K2PI	37	-1846.2465	3930.5117	0.0000	1.0000
HKY	39	-1839.8696	3930.6238	0.0000	1.0000
GTR	43	-1832.0885	3940.7934	0.0000	1.0000
SYMG	41	-1840.0923	3943.9352	0.0000	1.0000
F81G	39	-1846.9444	3944.7734	0.0000	1.0000
SYMI	41	-1842.8755	3949.5016	0.0000	1.0000
SYMIG	42	-1839.7316	3949.6467	0.0000	1.0000
F81I	39	-1849.6343	3950.1533	0.0000	1.0000
F81IG	40	-1846.6215	3950.5606	0.0000	1.0000
K2P	36	-1861.6279	3954.8415	0.0000	1.0000
JC69G	36	-1865.3137	3962.2132	0.0000	1.0000
JC69I	36	-1868.0103	3967.6063	0.0000	1.0000
JC69IG	37	-1865.0290	3968.0768	0.0000	1.0000
SYM	40	-1858.4270	3974.1716	0.0000	1.0000
F81	38	-1865.1417	3974.7350	0.0000	1.0000
JC69	35	-1883.0760	3991.3050	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_3428.phylip = 1 - 622;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3428.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/chr11_3428.phylip = 1 - 622;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3428.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/chr11_3428.phylip = 1 - 622;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3428.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

