
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:09 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_24798.phylip" (19 taxa, 960 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	-3741.2099	7574.7477	0.4666	0.4666
HKYG	40	-3745.9663	7575.5017	0.3201	0.7867
GTRIG	45	-3741.5981	7577.7257	0.1053	0.8920
HKYIG	41	-3746.1054	7577.9624	0.0935	0.9855
HKYI	40	-3749.3659	7582.3008	0.0107	0.9962
GTRI	44	-3746.0155	7584.3588	0.0038	1.0000
K2PG	37	-3790.6668	7658.3835	0.0000	1.0000
K2PI	37	-3791.6877	7660.4253	0.0000	1.0000
K2PIG	38	-3790.9653	7661.1488	0.0000	1.0000
SYMG	41	-3788.0650	7661.8816	0.0000	1.0000
SYMIG	42	-3787.7015	7663.3419	0.0000	1.0000
SYMI	41	-3789.0422	7663.8360	0.0000	1.0000
HKY	39	-3803.8834	7689.1581	0.0000	1.0000
GTR	43	-3800.7065	7691.5441	0.0000	1.0000
F81G	39	-3838.7851	7758.9615	0.0000	1.0000
F81IG	40	-3838.3046	7760.1784	0.0000	1.0000
F81I	39	-3840.3221	7762.0355	0.0000	1.0000
K2P	36	-3847.6708	7770.2279	0.0000	1.0000
SYM	40	-3845.1783	7773.9256	0.0000	1.0000
JC69G	36	-3873.2770	7821.4402	0.0000	1.0000
JC69I	36	-3873.8364	7822.5591	0.0000	1.0000
JC69IG	37	-3872.9499	7822.9497	0.0000	1.0000
F81	38	-3893.9830	7867.1843	0.0000	1.0000
JC69	35	-3928.3147	7929.3566	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3741.2099	7570.4198	0.5283	0.5283
HKYG	40	-3745.9663	7571.9326	0.2479	0.7762
GTRIG	45	-3741.5981	7573.1961	0.1318	0.9080
HKYIG	41	-3746.1054	7574.2108	0.0794	0.9874
HKYI	40	-3749.3659	7578.7317	0.0083	0.9957
GTRI	44	-3746.0155	7580.0310	0.0043	1.0000
K2PG	37	-3790.6668	7655.3336	0.0000	1.0000
K2PI	37	-3791.6877	7657.3754	0.0000	1.0000
K2PIG	38	-3790.9653	7657.9306	0.0000	1.0000
SYMG	41	-3788.0650	7658.1299	0.0000	1.0000
SYMIG	42	-3787.7015	7659.4030	0.0000	1.0000
SYMI	41	-3789.0422	7660.0844	0.0000	1.0000
HKY	39	-3803.8834	7685.7668	0.0000	1.0000
GTR	43	-3800.7065	7687.4131	0.0000	1.0000
F81G	39	-3838.7851	7755.5702	0.0000	1.0000
F81IG	40	-3838.3046	7756.6093	0.0000	1.0000
F81I	39	-3840.3221	7758.6442	0.0000	1.0000
K2P	36	-3847.6708	7767.3416	0.0000	1.0000
SYM	40	-3845.1783	7770.3565	0.0000	1.0000
JC69G	36	-3873.2770	7818.5540	0.0000	1.0000
JC69I	36	-3873.8364	7819.6729	0.0000	1.0000
JC69IG	37	-3872.9499	7819.8998	0.0000	1.0000
F81	38	-3893.9830	7863.9661	0.0000	1.0000
JC69	35	-3928.3147	7926.6294	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3745.9663	7766.6100	0.9420	0.9420
HKYI	40	-3749.3659	7773.4091	0.0315	0.9734
HKYIG	41	-3746.1054	7773.7550	0.0265	0.9999
GTRG	44	-3741.2099	7784.5649	0.0001	1.0000
GTRIG	45	-3741.5981	7792.2081	0.0000	1.0000
GTRI	44	-3746.0155	7794.1760	0.0000	1.0000
K2PG	37	-3790.6668	7835.4101	0.0000	1.0000
K2PI	37	-3791.6877	7837.4519	0.0000	1.0000
K2PIG	38	-3790.9653	7842.8741	0.0000	1.0000
SYMG	41	-3788.0650	7857.6742	0.0000	1.0000
SYMI	41	-3789.0422	7859.6286	0.0000	1.0000
SYMIG	42	-3787.7015	7863.8142	0.0000	1.0000
HKY	39	-3803.8834	7875.5772	0.0000	1.0000
GTR	43	-3800.7065	7896.6912	0.0000	1.0000
K2P	36	-3847.6708	7942.5512	0.0000	1.0000
F81G	39	-3838.7851	7945.3806	0.0000	1.0000
F81I	39	-3840.3221	7948.4546	0.0000	1.0000
F81IG	40	-3838.3046	7951.2866	0.0000	1.0000
SYM	40	-3845.1783	7965.0339	0.0000	1.0000
JC69G	36	-3873.2770	7993.7636	0.0000	1.0000
JC69I	36	-3873.8364	7994.8825	0.0000	1.0000
JC69IG	37	-3872.9499	7999.9763	0.0000	1.0000
F81	38	-3893.9830	8048.9095	0.0000	1.0000
JC69	35	-3928.3147	8096.9720	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_24798.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24798.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_24798.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24798.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_24798.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24798.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

