
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:12 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_8770.phylip" (19 taxa, 577 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	-1822.1189	3739.6813	0.5363	0.5363
GTRI	44	-1823.0296	3741.5027	0.2157	0.7520
GTRIG	45	-1822.2645	3742.3255	0.1430	0.8949
HKYG	40	-1828.9165	3743.9524	0.0634	0.9583
HKYI	40	-1829.7937	3745.7067	0.0264	0.9847
HKYIG	41	-1829.1759	3746.7892	0.0153	1.0000
GTR	43	-1852.6224	3798.3442	0.0000	1.0000
HKY	39	-1858.5393	3800.8886	0.0000	1.0000
K2PG	37	-1869.4407	3818.0984	0.0000	1.0000
SYMG	41	-1865.3004	3819.0381	0.0000	1.0000
K2PIG	38	-1869.4888	3820.4870	0.0000	1.0000
K2PI	37	-1870.9042	3821.0254	0.0000	1.0000
SYMIG	42	-1865.3265	3821.4171	0.0000	1.0000
SYMI	41	-1866.9580	3822.3533	0.0000	1.0000
F81G	39	-1875.3006	3834.4113	0.0000	1.0000
F81I	39	-1876.4186	3836.6473	0.0000	1.0000
F81IG	40	-1876.3625	3838.8443	0.0000	1.0000
K2P	36	-1900.1448	3877.2229	0.0000	1.0000
SYM	40	-1896.8791	3879.8776	0.0000	1.0000
F81	38	-1904.0875	3889.6844	0.0000	1.0000
JC69G	36	-1908.0177	3892.9688	0.0000	1.0000
JC69IG	37	-1909.3327	3897.8825	0.0000	1.0000
JC69I	36	-1910.9246	3898.7825	0.0000	1.0000
JC69	35	-1937.6313	3949.9207	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1822.1189	3732.2377	0.5483	0.5483
GTRI	44	-1823.0296	3734.0591	0.2205	0.7688
GTRIG	45	-1822.2645	3734.5289	0.1744	0.9432
HKYG	40	-1828.9165	3737.8330	0.0334	0.9766
HKYI	40	-1829.7937	3739.5873	0.0139	0.9905
HKYIG	41	-1829.1759	3740.3518	0.0095	1.0000
GTR	43	-1852.6224	3791.2447	0.0000	1.0000
HKY	39	-1858.5393	3795.0786	0.0000	1.0000
SYMG	41	-1865.3004	3812.6007	0.0000	1.0000
K2PG	37	-1869.4407	3812.8814	0.0000	1.0000
SYMIG	42	-1865.3265	3814.6531	0.0000	1.0000
K2PIG	38	-1869.4888	3814.9777	0.0000	1.0000
K2PI	37	-1870.9042	3815.8084	0.0000	1.0000
SYMI	41	-1866.9580	3815.9159	0.0000	1.0000
F81G	39	-1875.3006	3828.6012	0.0000	1.0000
F81I	39	-1876.4186	3830.8372	0.0000	1.0000
F81IG	40	-1876.3625	3832.7249	0.0000	1.0000
K2P	36	-1900.1448	3872.2896	0.0000	1.0000
SYM	40	-1896.8791	3873.7582	0.0000	1.0000
F81	38	-1904.0875	3884.1751	0.0000	1.0000
JC69G	36	-1908.0177	3888.0354	0.0000	1.0000
JC69IG	37	-1909.3327	3892.6654	0.0000	1.0000
JC69I	36	-1910.9246	3893.8492	0.0000	1.0000
JC69	35	-1937.6313	3945.2627	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1828.9165	3912.1467	0.6887	0.6887
HKYI	40	-1829.7937	3913.9010	0.2865	0.9752
HKYIG	41	-1829.1759	3919.0233	0.0221	0.9973
GTRG	44	-1822.1189	3923.9828	0.0019	0.9992
GTRI	44	-1823.0296	3925.8042	0.0007	0.9999
GTRIG	45	-1822.2645	3930.6318	0.0001	1.0000
HKY	39	-1858.5393	3965.0344	0.0000	1.0000
K2PG	37	-1869.4407	3974.1215	0.0000	1.0000
K2PI	37	-1870.9042	3977.0485	0.0000	1.0000
GTR	43	-1852.6224	3978.6320	0.0000	1.0000
K2PIG	38	-1869.4888	3980.5757	0.0000	1.0000
SYMG	41	-1865.3004	3991.2723	0.0000	1.0000
SYMI	41	-1866.9580	3994.5875	0.0000	1.0000
SYMIG	42	-1865.3265	3997.6825	0.0000	1.0000
F81G	39	-1875.3006	3998.5570	0.0000	1.0000
F81I	39	-1876.4186	4000.7930	0.0000	1.0000
F81IG	40	-1876.3625	4007.0386	0.0000	1.0000
K2P	36	-1900.1448	4029.1719	0.0000	1.0000
JC69G	36	-1908.0177	4044.9177	0.0000	1.0000
SYM	40	-1896.8791	4048.0719	0.0000	1.0000
F81	38	-1904.0875	4049.7731	0.0000	1.0000
JC69I	36	-1910.9246	4050.7315	0.0000	1.0000
JC69IG	37	-1909.3327	4053.9056	0.0000	1.0000
JC69	35	-1937.6313	4097.7871	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_8770.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8770.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_8770.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8770.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_8770.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8770.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;


-------------------------------------------------------------
End of Output

