
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:31 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/chr6_8057.phylip" (19 taxa, 722 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	-2725.3405	5544.5304	0.5731	0.5731
GTRIG	45	-2724.8538	5545.8318	0.2990	0.8721
HKYG	40	-2731.8461	5548.5087	0.0784	0.9505
HKYIG	41	-2731.2063	5549.4774	0.0483	0.9988
GTRI	44	-2731.6500	5557.1493	0.0010	0.9998
HKYI	40	-2737.9882	5560.7928	0.0002	1.0000
K2PG	37	-2777.3224	5632.7558	0.0000	1.0000
K2PIG	38	-2776.8254	5633.9906	0.0000	1.0000
SYMG	41	-2773.7660	5634.5967	0.0000	1.0000
SYMIG	42	-2773.4021	5636.1238	0.0000	1.0000
K2PI	37	-2783.4916	5645.0943	0.0000	1.0000
SYMI	41	-2779.7951	5646.6548	0.0000	1.0000
F81G	39	-2783.1951	5648.9649	0.0000	1.0000
F81IG	40	-2782.7482	5650.3129	0.0000	1.0000
GTR	43	-2782.6012	5656.7836	0.0000	1.0000
HKY	39	-2788.7384	5660.0516	0.0000	1.0000
F81I	39	-2788.9218	5660.4184	0.0000	1.0000
JC69G	36	-2817.8692	5711.6274	0.0000	1.0000
JC69IG	37	-2817.4601	5713.0313	0.0000	1.0000
JC69I	36	-2823.7670	5723.4230	0.0000	1.0000
SYM	40	-2823.9635	5732.7435	0.0000	1.0000
K2P	36	-2829.7712	5735.4315	0.0000	1.0000
F81	38	-2834.9425	5750.2246	0.0000	1.0000
JC69	35	-2868.5134	5810.7003	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2725.3405	5538.6811	0.5750	0.5750
GTRIG	45	-2724.8538	5539.7075	0.3442	0.9192
HKYG	40	-2731.8461	5543.6922	0.0469	0.9661
HKYIG	41	-2731.2063	5544.4127	0.0327	0.9989
GTRI	44	-2731.6500	5551.2999	0.0010	0.9999
HKYI	40	-2737.9882	5555.9764	0.0001	1.0000
K2PG	37	-2777.3224	5628.6447	0.0000	1.0000
SYMG	41	-2773.7660	5629.5320	0.0000	1.0000
K2PIG	38	-2776.8254	5629.6509	0.0000	1.0000
SYMIG	42	-2773.4021	5630.8042	0.0000	1.0000
K2PI	37	-2783.4916	5640.9832	0.0000	1.0000
SYMI	41	-2779.7951	5641.5901	0.0000	1.0000
F81G	39	-2783.1951	5644.3901	0.0000	1.0000
F81IG	40	-2782.7482	5645.4965	0.0000	1.0000
GTR	43	-2782.6012	5651.2025	0.0000	1.0000
HKY	39	-2788.7384	5655.4768	0.0000	1.0000
F81I	39	-2788.9218	5655.8436	0.0000	1.0000
JC69G	36	-2817.8692	5707.7383	0.0000	1.0000
JC69IG	37	-2817.4601	5708.9202	0.0000	1.0000
JC69I	36	-2823.7670	5719.5339	0.0000	1.0000
SYM	40	-2823.9635	5727.9271	0.0000	1.0000
K2P	36	-2829.7712	5731.5425	0.0000	1.0000
F81	38	-2834.9425	5745.8849	0.0000	1.0000
JC69	35	-2868.5134	5807.0268	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2731.8461	5726.9732	0.9310	0.9310
HKYIG	41	-2731.2063	5732.2757	0.0657	0.9967
HKYI	40	-2737.9882	5739.2574	0.0020	0.9987
GTRG	44	-2725.3405	5740.2902	0.0012	0.9999
GTRIG	45	-2724.8538	5745.8987	0.0001	1.0000
GTRI	44	-2731.6500	5752.9090	0.0000	1.0000
K2PG	37	-2777.3224	5798.1797	0.0000	1.0000
K2PIG	38	-2776.8254	5803.7678	0.0000	1.0000
K2PI	37	-2783.4916	5810.5181	0.0000	1.0000
SYMG	41	-2773.7660	5817.3951	0.0000	1.0000
F81G	39	-2783.1951	5823.0891	0.0000	1.0000
SYMIG	42	-2773.4021	5823.2492	0.0000	1.0000
F81IG	40	-2782.7482	5828.7775	0.0000	1.0000
SYMI	41	-2779.7951	5829.4532	0.0000	1.0000
HKY	39	-2788.7384	5834.1758	0.0000	1.0000
F81I	39	-2788.9218	5834.5426	0.0000	1.0000
GTR	43	-2782.6012	5848.2295	0.0000	1.0000
JC69G	36	-2817.8692	5872.6912	0.0000	1.0000
JC69IG	37	-2817.4601	5878.4552	0.0000	1.0000
JC69I	36	-2823.7670	5884.4868	0.0000	1.0000
K2P	36	-2829.7712	5896.4954	0.0000	1.0000
SYM	40	-2823.9635	5911.2081	0.0000	1.0000
F81	38	-2834.9425	5920.0019	0.0000	1.0000
JC69	35	-2868.5134	5967.3977	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/chr6_8057.phylip = 1 - 722;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8057.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/chr6_8057.phylip = 1 - 722;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8057.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/chr6_8057.phylip = 1 - 722;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8057.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

