
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:44 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_4118.phylip" (19 taxa, 213 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKYI
Minimum BIC  model: F81


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	-467.1426	1033.3549	0.1813	0.1813
HKYG	40	-467.2885	1033.6467	0.1567	0.3380
HKY	39	-468.8648	1033.7643	0.1477	0.4857
GTR	43	-462.8956	1034.1818	0.1199	0.6056
F81I	39	-469.5166	1035.0678	0.0770	0.6826
GTRI	44	-461.7830	1035.1374	0.0744	0.7570
F81G	39	-469.6432	1035.3212	0.0678	0.8248
GTRG	44	-461.9917	1035.5548	0.0604	0.8852
F81	38	-471.4213	1035.8770	0.0514	0.9365
HKYIG	41	-467.2881	1036.7165	0.0338	0.9703
F81IG	40	-469.6429	1038.3556	0.0149	0.9852
GTRIG	45	-461.7892	1038.3689	0.0148	0.9999
JC69I	36	-482.4434	1052.0233	0.0000	1.0000
JC69G	36	-482.5374	1052.2112	0.0000	1.0000
JC69	35	-484.7377	1053.7128	0.0000	1.0000
K2PG	37	-482.3730	1054.8146	0.0000	1.0000
K2PI	37	-482.4646	1054.9978	0.0000	1.0000
JC69IG	37	-482.5370	1055.1427	0.0000	1.0000
K2P	36	-484.8326	1056.8016	0.0000	1.0000
K2PIG	38	-482.3424	1057.7193	0.0000	1.0000
SYMI	41	-478.2401	1058.6206	0.0000	1.0000
SYM	40	-479.7952	1058.6602	0.0000	1.0000
SYMG	41	-478.4021	1058.9446	0.0000	1.0000
SYMIG	42	-478.4235	1062.0940	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-461.7830	1011.5660	0.2548	0.2548
GTR	43	-462.8956	1011.7912	0.2276	0.4824
GTRG	44	-461.9917	1011.9834	0.2068	0.6891
GTRIG	45	-461.7892	1013.5784	0.0931	0.7823
HKYI	40	-467.1426	1014.2851	0.0654	0.8477
HKYG	40	-467.2885	1014.5769	0.0565	0.9042
HKY	39	-468.8648	1015.7296	0.0318	0.9360
HKYIG	41	-467.2881	1016.5761	0.0208	0.9568
F81I	39	-469.5166	1017.0331	0.0166	0.9733
F81G	39	-469.6432	1017.2865	0.0146	0.9879
F81	38	-471.4213	1018.8426	0.0067	0.9946
F81IG	40	-469.6429	1019.2859	0.0054	1.0000
JC69I	36	-482.4434	1036.8869	0.0000	1.0000
JC69G	36	-482.5374	1037.0748	0.0000	1.0000
SYMI	41	-478.2401	1038.4802	0.0000	1.0000
K2PG	37	-482.3730	1038.7460	0.0000	1.0000
SYMG	41	-478.4021	1038.8042	0.0000	1.0000
K2PI	37	-482.4646	1038.9292	0.0000	1.0000
JC69IG	37	-482.5370	1039.0741	0.0000	1.0000
JC69	35	-484.7377	1039.4755	0.0000	1.0000
SYM	40	-479.7952	1039.5904	0.0000	1.0000
K2PIG	38	-482.3424	1040.6848	0.0000	1.0000
SYMIG	42	-478.4235	1040.8469	0.0000	1.0000
K2P	36	-484.8326	1041.6652	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
F81	38	-471.4213	1146.5717	0.2897	0.2897
HKY	39	-468.8648	1146.8200	0.2559	0.5456
F81I	39	-469.5166	1148.1235	0.1333	0.6789
F81G	39	-469.6432	1148.3769	0.1175	0.7964
HKYI	40	-467.1426	1148.7368	0.0981	0.8945
HKYG	40	-467.2885	1149.0286	0.0848	0.9794
F81IG	40	-469.6429	1153.7376	0.0081	0.9874
HKYIG	41	-467.2881	1154.3891	0.0058	0.9932
GTR	43	-462.8956	1156.3268	0.0022	0.9954
JC69	35	-484.7377	1157.1207	0.0015	0.9969
JC69I	36	-482.4434	1157.8934	0.0010	0.9979
JC69G	36	-482.5374	1158.0813	0.0009	0.9988
GTRI	44	-461.7830	1159.4628	0.0005	0.9993
GTRG	44	-461.9917	1159.8803	0.0004	0.9997
K2P	36	-484.8326	1162.6717	0.0001	0.9998
K2PG	37	-482.3730	1163.1138	0.0001	0.9998
K2PI	37	-482.4646	1163.2970	0.0001	0.9999
JC69IG	37	-482.5370	1163.4419	0.0001	1.0000
GTRIG	45	-461.7892	1164.8366	0.0000	1.0000
K2PIG	38	-482.3424	1168.4139	0.0000	1.0000
SYM	40	-479.7952	1174.0421	0.0000	1.0000
SYMI	41	-478.2401	1176.2932	0.0000	1.0000
SYMG	41	-478.4021	1176.6172	0.0000	1.0000
SYMIG	42	-478.4235	1182.0212	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4118.phylip = 1 - 213;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4118.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) 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/chr6_4118.phylip = 1 - 213;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4118.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 (F81)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4118.phylip = 1 - 213;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4118.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=1 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0);
END;


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End of Output

