
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:38 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_9601.phylip" (19 taxa, 169 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: F81G


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
HKYG	40	-471.0346	1047.6941	0.3292	0.3292
F81G	39	-473.1756	1048.5372	0.2160	0.5452
HKYI	40	-471.9562	1049.5374	0.1310	0.6762
F81I	39	-474.0736	1050.3333	0.0880	0.7642
HKYIG	41	-470.9189	1050.9560	0.0644	0.8286
GTRG	44	-465.8112	1051.5578	0.0477	0.8763
F81IG	40	-473.0656	1051.7562	0.0432	0.9195
HKY	39	-475.1603	1052.5067	0.0297	0.9492
F81	38	-477.2553	1053.3107	0.0199	0.9691
GTRI	44	-466.7709	1053.4772	0.0183	0.9873
GTRIG	45	-465.7241	1055.1067	0.0081	0.9954
GTR	43	-470.3622	1056.9963	0.0031	0.9986
JC69G	36	-484.3065	1060.7948	0.0005	0.9990
K2PG	37	-482.9023	1061.2702	0.0004	0.9994
JC69I	36	-485.2325	1062.6468	0.0002	0.9996
K2PI	37	-483.8603	1063.1862	0.0001	0.9997
JC69IG	37	-484.1667	1063.7990	0.0001	0.9999
K2PIG	38	-482.7422	1064.2843	0.0001	0.9999
JC69	35	-488.5654	1066.0781	0.0000	1.0000
K2P	36	-487.2637	1066.7092	0.0000	1.0000
SYMG	41	-480.2767	1069.6715	0.0000	1.0000
SYMI	41	-481.2144	1071.5469	0.0000	1.0000
SYMIG	42	-480.1482	1072.9631	0.0000	1.0000
SYM	40	-484.5526	1074.7302	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-465.8112	1019.6223	0.3946	0.3946
GTRIG	45	-465.7241	1021.4482	0.1584	0.5530
GTRI	44	-466.7709	1021.5417	0.1511	0.7041
HKYG	40	-471.0346	1022.0691	0.1161	0.8202
HKYIG	41	-470.9189	1023.8379	0.0479	0.8682
HKYI	40	-471.9562	1023.9124	0.0462	0.9144
F81G	39	-473.1756	1024.3512	0.0371	0.9515
F81IG	40	-473.0656	1026.1312	0.0152	0.9667
F81I	39	-474.0736	1026.1472	0.0151	0.9818
GTR	43	-470.3622	1026.7243	0.0113	0.9931
HKY	39	-475.1603	1028.3207	0.0051	0.9982
F81	38	-477.2553	1030.5107	0.0017	0.9999
K2PG	37	-482.9023	1039.8046	0.0000	1.0000
JC69G	36	-484.3065	1040.6130	0.0000	1.0000
K2PIG	38	-482.7422	1041.4843	0.0000	1.0000
K2PI	37	-483.8603	1041.7206	0.0000	1.0000
JC69IG	37	-484.1667	1042.3333	0.0000	1.0000
JC69I	36	-485.2325	1042.4650	0.0000	1.0000
SYMG	41	-480.2767	1042.5534	0.0000	1.0000
SYMIG	42	-480.1482	1044.2964	0.0000	1.0000
SYMI	41	-481.2144	1044.4287	0.0000	1.0000
K2P	36	-487.2637	1046.5274	0.0000	1.0000
JC69	35	-488.5654	1047.1308	0.0000	1.0000
SYM	40	-484.5526	1049.1052	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
F81G	39	-473.1756	1146.4172	0.3449	0.3449
HKYG	40	-471.0346	1147.2651	0.2258	0.5707
F81I	39	-474.0736	1148.2133	0.1405	0.7112
HKYI	40	-471.9562	1149.1083	0.0898	0.8011
F81	38	-477.2553	1149.4468	0.0758	0.8769
HKY	39	-475.1603	1150.3867	0.0474	0.9243
F81IG	40	-473.0656	1151.3272	0.0296	0.9539
HKYIG	41	-470.9189	1152.1637	0.0195	0.9734
JC69G	36	-484.3065	1153.2893	0.0111	0.9845
JC69I	36	-485.2325	1155.1414	0.0044	0.9889
K2PG	37	-482.9023	1155.6108	0.0035	0.9924
JC69	35	-488.5654	1156.6772	0.0020	0.9944
GTRG	44	-465.8112	1157.3379	0.0015	0.9959
K2PI	37	-483.8603	1157.5268	0.0013	0.9972
JC69IG	37	-484.1667	1158.1396	0.0010	0.9982
K2P	36	-487.2637	1159.2038	0.0006	0.9988
GTRI	44	-466.7709	1159.2573	0.0006	0.9994
K2PIG	38	-482.7422	1160.4205	0.0003	0.9997
GTR	43	-470.3622	1161.3100	0.0002	0.9999
GTRIG	45	-465.7241	1162.2936	0.0001	1.0000
SYMG	41	-480.2767	1170.8793	0.0000	1.0000
SYMI	41	-481.2144	1172.7546	0.0000	1.0000
SYM	40	-484.5526	1174.3012	0.0000	1.0000
SYMIG	42	-480.1482	1175.7522	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_9601.phylip = 1 - 169;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9601.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9601.phylip = 1 - 169;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9601.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;


[Mrbayes block for the best BIC model (F81G)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9601.phylip = 1 - 169;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9601.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=1 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

