
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:50 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_11806.phylip" (19 taxa, 599 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-1863.4693	3815.1218	0.6702	0.6702
HKYG	40	-1866.0172	3817.9126	0.1660	0.8362
HKYI	40	-1866.8420	3819.5622	0.0728	0.9089
GTRIG	45	-1861.1409	3819.7682	0.0656	0.9746
GTRG	44	-1863.6695	3822.4870	0.0169	0.9915
GTRI	44	-1864.5554	3824.2589	0.0070	0.9984
K2PIG	38	-1873.2534	3827.7997	0.0012	0.9996
K2PG	37	-1876.0303	3831.0731	0.0002	0.9998
K2PI	37	-1876.8782	3832.7689	0.0001	0.9999
SYMIG	42	-1871.5791	3833.6546	0.0001	1.0000
SYMG	41	-1874.3937	3836.9706	0.0000	1.0000
SYMI	41	-1875.2905	3838.7642	0.0000	1.0000
F81IG	40	-1912.1837	3910.2456	0.0000	1.0000
F81G	39	-1914.3753	3912.3320	0.0000	1.0000
F81I	39	-1915.1868	3913.9549	0.0000	1.0000
JC69IG	37	-1921.0397	3921.0919	0.0000	1.0000
JC69G	36	-1923.3495	3923.4392	0.0000	1.0000
JC69I	36	-1924.1932	3925.1266	0.0000	1.0000
HKY	39	-1940.1505	3963.8824	0.0000	1.0000
GTR	43	-1937.7643	3968.3465	0.0000	1.0000
K2P	36	-1949.9340	3976.6083	0.0000	1.0000
SYM	40	-1947.8156	3981.5093	0.0000	1.0000
F81	38	-1987.0495	4055.3919	0.0000	1.0000
JC69	35	-1995.9175	4066.3110	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1863.4693	3808.9386	0.6439	0.6439
HKYG	40	-1866.0172	3812.0345	0.1370	0.7809
GTRIG	45	-1861.1409	3812.2817	0.1210	0.9019
HKYI	40	-1866.8420	3813.6841	0.0600	0.9619
GTRG	44	-1863.6695	3815.3390	0.0262	0.9882
GTRI	44	-1864.5554	3817.1109	0.0108	0.9990
K2PIG	38	-1873.2534	3822.5069	0.0007	0.9997
K2PG	37	-1876.0303	3826.0606	0.0001	0.9999
SYMIG	42	-1871.5791	3827.1582	0.0001	0.9999
K2PI	37	-1876.8782	3827.7565	0.0001	1.0000
SYMG	41	-1874.3937	3830.7874	0.0000	1.0000
SYMI	41	-1875.2905	3832.5811	0.0000	1.0000
F81IG	40	-1912.1837	3904.3674	0.0000	1.0000
F81G	39	-1914.3753	3906.7506	0.0000	1.0000
F81I	39	-1915.1868	3908.3735	0.0000	1.0000
JC69IG	37	-1921.0397	3916.0794	0.0000	1.0000
JC69G	36	-1923.3495	3918.6990	0.0000	1.0000
JC69I	36	-1924.1932	3920.3864	0.0000	1.0000
HKY	39	-1940.1505	3958.3010	0.0000	1.0000
GTR	43	-1937.7643	3961.5285	0.0000	1.0000
K2P	36	-1949.9340	3971.8681	0.0000	1.0000
SYM	40	-1947.8156	3975.6312	0.0000	1.0000
F81	38	-1987.0495	4050.0991	0.0000	1.0000
JC69	35	-1995.9175	4061.8350	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1866.0172	3987.8449	0.3003	0.3003
K2PG	37	-1876.0303	3988.6853	0.1973	0.4975
HKYIG	41	-1863.4693	3989.1444	0.1568	0.6544
HKYI	40	-1866.8420	3989.4945	0.1316	0.7860
K2PIG	38	-1873.2534	3989.5268	0.1295	0.9155
K2PI	37	-1876.8782	3990.3811	0.0845	1.0000
GTRG	44	-1863.6695	4008.7305	0.0000	1.0000
GTRIG	45	-1861.1409	4010.0685	0.0000	1.0000
GTRI	44	-1864.5554	4010.5024	0.0000	1.0000
SYMG	41	-1874.3937	4010.9932	0.0000	1.0000
SYMIG	42	-1871.5791	4011.7592	0.0000	1.0000
SYMI	41	-1875.2905	4012.7868	0.0000	1.0000
JC69G	36	-1923.3495	4076.9284	0.0000	1.0000
F81G	39	-1914.3753	4078.1658	0.0000	1.0000
JC69I	36	-1924.1932	4078.6158	0.0000	1.0000
JC69IG	37	-1921.0397	4078.7041	0.0000	1.0000
F81I	39	-1915.1868	4079.7887	0.0000	1.0000
F81IG	40	-1912.1837	4080.1779	0.0000	1.0000
HKY	39	-1940.1505	4129.7162	0.0000	1.0000
K2P	36	-1949.9340	4130.0975	0.0000	1.0000
GTR	43	-1937.7643	4150.5248	0.0000	1.0000
SYM	40	-1947.8156	4151.4416	0.0000	1.0000
JC69	35	-1995.9175	4215.6692	0.0000	1.0000
F81	38	-1987.0495	4217.1190	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11806.phylip = 1 - 599;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11806.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11806.phylip = 1 - 599;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11806.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_11806.phylip = 1 - 599;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11806.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

