
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_24800.phylip" (19 taxa, 689 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: K2PG


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
HKYI	40	-1880.2356	3845.5328	0.4183	0.4183
HKYG	40	-1880.2634	3845.5886	0.4068	0.8251
HKYIG	41	-1880.2824	3847.8879	0.1289	0.9540
GTRI	44	-1879.0540	3852.2572	0.0145	0.9685
GTRG	44	-1879.1095	3852.3681	0.0137	0.9822
K2PG	37	-1887.8712	3854.0618	0.0059	0.9881
K2PI	37	-1887.9325	3854.1846	0.0055	0.9936
GTRIG	45	-1879.1415	3854.7216	0.0042	0.9978
K2PIG	38	-1887.8832	3856.3264	0.0019	0.9997
SYMG	41	-1887.2193	3861.7616	0.0001	0.9998
SYMI	41	-1887.2766	3861.8762	0.0001	1.0000
SYMIG	42	-1887.2327	3864.0567	0.0000	1.0000
HKY	39	-1896.2847	3875.3768	0.0000	1.0000
GTR	43	-1895.3173	3882.5012	0.0000	1.0000
K2P	36	-1903.3801	3882.8462	0.0000	1.0000
SYM	40	-1902.4965	3890.0547	0.0000	1.0000
F81I	39	-1923.5967	3930.0008	0.0000	1.0000
F81G	39	-1923.6005	3930.0084	0.0000	1.0000
F81IG	40	-1923.6297	3932.3211	0.0000	1.0000
JC69G	36	-1930.0263	3936.1385	0.0000	1.0000
JC69I	36	-1930.0532	3936.1924	0.0000	1.0000
JC69IG	37	-1930.0473	3938.4140	0.0000	1.0000
F81	38	-1938.8260	3958.2121	0.0000	1.0000
JC69	35	-1944.9575	3963.7741	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1880.2356	3840.4711	0.4027	0.4027
HKYG	40	-1880.2634	3840.5269	0.3917	0.7944
HKYIG	41	-1880.2824	3842.5649	0.1414	0.9358
GTRI	44	-1879.0540	3846.1081	0.0240	0.9598
GTRG	44	-1879.1095	3846.2191	0.0227	0.9826
GTRIG	45	-1879.1415	3848.2831	0.0081	0.9907
K2PG	37	-1887.8712	3849.7423	0.0039	0.9946
K2PI	37	-1887.9325	3849.8651	0.0037	0.9983
K2PIG	38	-1887.8832	3851.7664	0.0014	0.9997
SYMG	41	-1887.2193	3856.4386	0.0001	0.9998
SYMI	41	-1887.2766	3856.5532	0.0001	1.0000
SYMIG	42	-1887.2327	3858.4654	0.0000	1.0000
HKY	39	-1896.2847	3870.5694	0.0000	1.0000
GTR	43	-1895.3173	3876.6346	0.0000	1.0000
K2P	36	-1903.3801	3878.7603	0.0000	1.0000
SYM	40	-1902.4965	3884.9930	0.0000	1.0000
F81I	39	-1923.5967	3925.1934	0.0000	1.0000
F81G	39	-1923.6005	3925.2010	0.0000	1.0000
F81IG	40	-1923.6297	3927.2593	0.0000	1.0000
JC69G	36	-1930.0263	3932.0526	0.0000	1.0000
JC69I	36	-1930.0532	3932.1065	0.0000	1.0000
JC69IG	37	-1930.0473	3934.0945	0.0000	1.0000
F81	38	-1938.8260	3953.6521	0.0000	1.0000
JC69	35	-1944.9575	3959.9150	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1887.8712	4017.5463	0.4529	0.4529
K2PI	37	-1887.9325	4017.6690	0.4259	0.8788
HKYI	40	-1880.2356	4021.8808	0.0518	0.9306
HKYG	40	-1880.2634	4021.9366	0.0504	0.9811
K2PIG	38	-1887.8832	4024.1056	0.0170	0.9981
HKYIG	41	-1880.2824	4028.5098	0.0019	1.0000
K2P	36	-1903.3801	4042.0290	0.0000	1.0000
SYMG	41	-1887.2193	4042.3835	0.0000	1.0000
SYMI	41	-1887.2766	4042.4981	0.0000	1.0000
GTRI	44	-1879.0540	4045.6587	0.0000	1.0000
GTRG	44	-1879.1095	4045.7697	0.0000	1.0000
HKY	39	-1896.2847	4047.4438	0.0000	1.0000
SYMIG	42	-1887.2327	4048.9455	0.0000	1.0000
GTRIG	45	-1879.1415	4052.3689	0.0000	1.0000
SYM	40	-1902.4965	4066.4027	0.0000	1.0000
GTR	43	-1895.3173	4071.6499	0.0000	1.0000
JC69G	36	-1930.0263	4095.3213	0.0000	1.0000
JC69I	36	-1930.0532	4095.3752	0.0000	1.0000
JC69IG	37	-1930.0473	4101.8984	0.0000	1.0000
F81I	39	-1923.5967	4102.0678	0.0000	1.0000
F81G	39	-1923.6005	4102.0754	0.0000	1.0000
F81IG	40	-1923.6297	4108.6690	0.0000	1.0000
JC69	35	-1944.9575	4118.6484	0.0000	1.0000
F81	38	-1938.8260	4125.9912	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip = 1 - 689;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip = 1 - 689;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip = 1 - 689;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24800.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

