
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:35 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/chr1_15477.phylip" (19 taxa, 546 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1363.9915	2814.4781	0.2909	0.2909
GTRG	44	-1359.4688	2814.8417	0.2425	0.5334
HKYI	40	-1364.6548	2815.8047	0.1499	0.6833
GTRI	44	-1360.0451	2815.9944	0.1363	0.8196
HKYIG	41	-1363.8868	2816.6070	0.1003	0.9199
GTRIG	45	-1359.3909	2817.0618	0.0799	0.9998
GTR	43	-1368.6629	2830.8637	0.0001	0.9999
HKY	39	-1373.4008	2830.9676	0.0001	1.0000
F81G	39	-1380.5185	2845.2029	0.0000	1.0000
F81I	39	-1381.1788	2846.5235	0.0000	1.0000
F81IG	40	-1380.3786	2847.2522	0.0000	1.0000
K2PG	37	-1389.2755	2858.0863	0.0000	1.0000
K2PI	37	-1389.8863	2859.3081	0.0000	1.0000
K2PIG	38	-1389.1686	2860.1833	0.0000	1.0000
SYMG	41	-1387.1704	2863.1740	0.0000	1.0000
F81	38	-1390.7321	2863.3103	0.0000	1.0000
SYMI	41	-1387.6665	2864.1663	0.0000	1.0000
SYMIG	42	-1387.1018	2865.3845	0.0000	1.0000
K2P	36	-1398.9275	2875.0887	0.0000	1.0000
SYM	40	-1396.6318	2879.7587	0.0000	1.0000
JC69G	36	-1404.5480	2886.3299	0.0000	1.0000
JC69I	36	-1405.2107	2887.6551	0.0000	1.0000
JC69IG	37	-1404.3855	2888.3065	0.0000	1.0000
JC69	35	-1415.1490	2905.2391	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1359.4688	2806.9375	0.3225	0.3225
HKYG	40	-1363.9915	2807.9831	0.1912	0.5137
GTRI	44	-1360.0451	2808.0902	0.1812	0.6950
GTRIG	45	-1359.3909	2808.7818	0.1283	0.8233
HKYI	40	-1364.6548	2809.3097	0.0985	0.9218
HKYIG	41	-1363.8868	2809.7737	0.0781	0.9999
GTR	43	-1368.6629	2823.3259	0.0001	1.0000
HKY	39	-1373.4008	2824.8016	0.0000	1.0000
F81G	39	-1380.5185	2839.0369	0.0000	1.0000
F81I	39	-1381.1788	2840.3575	0.0000	1.0000
F81IG	40	-1380.3786	2840.7571	0.0000	1.0000
K2PG	37	-1389.2755	2852.5509	0.0000	1.0000
K2PI	37	-1389.8863	2853.7727	0.0000	1.0000
K2PIG	38	-1389.1686	2854.3372	0.0000	1.0000
SYMG	41	-1387.1704	2856.3407	0.0000	1.0000
SYMI	41	-1387.6665	2857.3329	0.0000	1.0000
F81	38	-1390.7321	2857.4641	0.0000	1.0000
SYMIG	42	-1387.1018	2858.2036	0.0000	1.0000
K2P	36	-1398.9275	2869.8549	0.0000	1.0000
SYM	40	-1396.6318	2873.2637	0.0000	1.0000
JC69G	36	-1404.5480	2881.0961	0.0000	1.0000
JC69I	36	-1405.2107	2882.4213	0.0000	1.0000
JC69IG	37	-1404.3855	2882.7711	0.0000	1.0000
JC69	35	-1415.1490	2900.2979	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1363.9915	2980.0878	0.6389	0.6389
HKYI	40	-1364.6548	2981.4144	0.3292	0.9681
HKYIG	41	-1363.8868	2986.1810	0.0304	0.9985
HKY	39	-1373.4008	2992.6037	0.0012	0.9997
GTRG	44	-1359.4688	2996.2528	0.0002	0.9999
GTRI	44	-1360.0451	2997.4054	0.0001	1.0000
GTRIG	45	-1359.3909	3002.3996	0.0000	1.0000
F81G	39	-1380.5185	3006.8391	0.0000	1.0000
F81I	39	-1381.1788	3008.1597	0.0000	1.0000
GTR	43	-1368.6629	3008.3385	0.0000	1.0000
K2PG	37	-1389.2755	3011.7478	0.0000	1.0000
F81IG	40	-1380.3786	3012.8619	0.0000	1.0000
K2PI	37	-1389.8863	3012.9696	0.0000	1.0000
K2PIG	38	-1389.1686	3017.8367	0.0000	1.0000
F81	38	-1390.7321	3020.9636	0.0000	1.0000
K2P	36	-1398.9275	3024.7492	0.0000	1.0000
SYMG	41	-1387.1704	3032.7481	0.0000	1.0000
SYMI	41	-1387.6665	3033.7403	0.0000	1.0000
JC69G	36	-1404.5480	3035.9903	0.0000	1.0000
JC69I	36	-1405.2107	3037.3156	0.0000	1.0000
SYMIG	42	-1387.1018	3038.9136	0.0000	1.0000
JC69IG	37	-1404.3855	3041.9680	0.0000	1.0000
SYM	40	-1396.6318	3045.3684	0.0000	1.0000
JC69	35	-1415.1490	3050.8896	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/chr1_15477.phylip = 1 - 546;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15477.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/chr1_15477.phylip = 1 - 546;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15477.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15477.phylip = 1 - 546;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15477.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

