
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:32 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/chr3_764.phylip" (19 taxa, 717 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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	-1985.0631	4054.9783	0.2382	0.2382
GTRG	44	-1980.5719	4055.0366	0.2313	0.4695
GTRI	44	-1980.7045	4055.3019	0.2026	0.6721
HKYG	40	-1985.3435	4055.5391	0.1799	0.8520
GTRIG	45	-1980.3820	4056.9339	0.0896	0.9416
HKYIG	41	-1985.3432	4057.7885	0.0584	1.0000
F81I	39	-2005.5917	4093.7920	0.0000	1.0000
F81G	39	-2005.7853	4094.1791	0.0000	1.0000
F81IG	40	-2005.4769	4095.8059	0.0000	1.0000
GTR	43	-2008.6317	4108.8859	0.0000	1.0000
HKY	39	-2013.8193	4110.2472	0.0000	1.0000
F81	38	-2031.6223	4143.6163	0.0000	1.0000
SYMG	41	-2029.6688	4146.4397	0.0000	1.0000
SYMI	41	-2030.1438	4147.3898	0.0000	1.0000
SYMIG	42	-2029.4673	4148.2936	0.0000	1.0000
K2PI	37	-2035.8258	4149.7930	0.0000	1.0000
K2PG	37	-2035.8730	4149.8873	0.0000	1.0000
K2PIG	38	-2035.6319	4151.6354	0.0000	1.0000
JC69I	36	-2050.3016	4176.5207	0.0000	1.0000
JC69G	36	-2050.4191	4176.7558	0.0000	1.0000
JC69IG	37	-2050.4583	4179.0579	0.0000	1.0000
SYM	40	-2054.5215	4193.8951	0.0000	1.0000
K2P	36	-2060.9661	4197.8499	0.0000	1.0000
JC69	35	-2075.0199	4223.7402	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1980.5719	4049.1438	0.2805	0.2805
GTRI	44	-1980.7045	4049.4090	0.2457	0.5262
HKYI	40	-1985.0631	4050.1262	0.1716	0.6978
HKYG	40	-1985.3435	4050.6871	0.1297	0.8275
GTRIG	45	-1980.3820	4050.7640	0.1248	0.9523
HKYIG	41	-1985.3432	4052.6863	0.0477	1.0000
F81I	39	-2005.5917	4089.1834	0.0000	1.0000
F81G	39	-2005.7853	4089.5706	0.0000	1.0000
F81IG	40	-2005.4769	4090.9538	0.0000	1.0000
GTR	43	-2008.6317	4103.2633	0.0000	1.0000
HKY	39	-2013.8193	4105.6387	0.0000	1.0000
F81	38	-2031.6223	4139.2446	0.0000	1.0000
SYMG	41	-2029.6688	4141.3375	0.0000	1.0000
SYMI	41	-2030.1438	4142.2876	0.0000	1.0000
SYMIG	42	-2029.4673	4142.9346	0.0000	1.0000
K2PI	37	-2035.8258	4145.6516	0.0000	1.0000
K2PG	37	-2035.8730	4145.7459	0.0000	1.0000
K2PIG	38	-2035.6319	4147.2637	0.0000	1.0000
JC69I	36	-2050.3016	4172.6031	0.0000	1.0000
JC69G	36	-2050.4191	4172.8382	0.0000	1.0000
JC69IG	37	-2050.4583	4174.9165	0.0000	1.0000
SYM	40	-2054.5215	4189.0430	0.0000	1.0000
K2P	36	-2060.9661	4193.9323	0.0000	1.0000
JC69	35	-2075.0199	4220.0397	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1985.0631	4233.1293	0.5605	0.5605
HKYG	40	-1985.3435	4233.6901	0.4235	0.9840
HKYIG	41	-1985.3432	4240.2644	0.0158	0.9998
GTRG	44	-1980.5719	4250.4471	0.0001	0.9999
GTRI	44	-1980.7045	4250.7123	0.0001	1.0000
GTRIG	45	-1980.3820	4256.6424	0.0000	1.0000
F81I	39	-2005.5917	4267.6114	0.0000	1.0000
F81G	39	-2005.7853	4267.9985	0.0000	1.0000
F81IG	40	-2005.4769	4273.9569	0.0000	1.0000
HKY	39	-2013.8193	4284.0666	0.0000	1.0000
GTR	43	-2008.6317	4299.9916	0.0000	1.0000
F81	38	-2031.6223	4313.0975	0.0000	1.0000
K2PI	37	-2035.8258	4314.9294	0.0000	1.0000
K2PG	37	-2035.8730	4315.0237	0.0000	1.0000
K2PIG	38	-2035.6319	4321.1166	0.0000	1.0000
SYMG	41	-2029.6688	4328.9156	0.0000	1.0000
SYMI	41	-2030.1438	4329.8657	0.0000	1.0000
SYMIG	42	-2029.4673	4335.0877	0.0000	1.0000
JC69I	36	-2050.3016	4337.3058	0.0000	1.0000
JC69G	36	-2050.4191	4337.5409	0.0000	1.0000
JC69IG	37	-2050.4583	4344.1943	0.0000	1.0000
K2P	36	-2060.9661	4358.6350	0.0000	1.0000
SYM	40	-2054.5215	4372.0461	0.0000	1.0000
JC69	35	-2075.0199	4380.1674	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/chr3_764.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_764.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_764.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_764.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_764.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_764.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;


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End of Output

