
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:29 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_15365.phylip" (19 taxa, 464 characters)

Minimum AIC  model: HKYG
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	-1242.8134	2573.3809	0.5667	0.5667
HKYIG	41	-1242.5214	2575.2039	0.2277	0.7944
HKYI	40	-1244.1515	2576.0570	0.1487	0.9431
GTRG	44	-1241.0527	2579.5564	0.0258	0.9689
GTRIG	45	-1240.7837	2581.4716	0.0099	0.9788
F81G	39	-1248.2347	2581.8278	0.0083	0.9871
GTRI	44	-1242.3299	2582.1108	0.0072	0.9943
F81IG	40	-1247.9536	2583.6613	0.0033	0.9977
F81I	39	-1249.5167	2584.3919	0.0023	1.0000
HKY	39	-1253.6925	2592.7434	0.0000	1.0000
GTR	43	-1251.7499	2598.5093	0.0000	1.0000
F81	38	-1259.1224	2601.2189	0.0000	1.0000
K2PG	37	-1262.6778	2605.9565	0.0000	1.0000
K2PIG	38	-1262.3403	2607.6548	0.0000	1.0000
K2PI	37	-1263.9932	2608.5872	0.0000	1.0000
SYMG	41	-1260.1718	2610.5048	0.0000	1.0000
SYMIG	42	-1259.8326	2612.2448	0.0000	1.0000
JC69G	36	-1267.2341	2612.7072	0.0000	1.0000
SYMI	41	-1261.4325	2613.0262	0.0000	1.0000
JC69IG	37	-1266.9201	2614.4411	0.0000	1.0000
JC69I	36	-1268.5105	2615.2598	0.0000	1.0000
K2P	36	-1274.1459	2626.5307	0.0000	1.0000
SYM	40	-1271.9516	2631.6573	0.0000	1.0000
JC69	35	-1278.5475	2632.9829	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1242.8134	2565.6268	0.5092	0.5092
HKYIG	41	-1242.5214	2567.0428	0.2509	0.7601
HKYI	40	-1244.1515	2568.3029	0.1336	0.8937
GTRG	44	-1241.0527	2570.1054	0.0542	0.9479
GTRIG	45	-1240.7837	2571.5673	0.0261	0.9740
GTRI	44	-1242.3299	2572.6597	0.0151	0.9892
F81G	39	-1248.2347	2574.4693	0.0061	0.9953
F81IG	40	-1247.9536	2575.9071	0.0030	0.9983
F81I	39	-1249.5167	2577.0334	0.0017	1.0000
HKY	39	-1253.6925	2585.3849	0.0000	1.0000
GTR	43	-1251.7499	2589.4998	0.0000	1.0000
F81	38	-1259.1224	2594.2448	0.0000	1.0000
K2PG	37	-1262.6778	2599.3555	0.0000	1.0000
K2PIG	38	-1262.3403	2600.6807	0.0000	1.0000
K2PI	37	-1263.9932	2601.9863	0.0000	1.0000
SYMG	41	-1260.1718	2602.3437	0.0000	1.0000
SYMIG	42	-1259.8326	2603.6652	0.0000	1.0000
SYMI	41	-1261.4325	2604.8651	0.0000	1.0000
JC69G	36	-1267.2341	2606.4683	0.0000	1.0000
JC69IG	37	-1266.9201	2607.8402	0.0000	1.0000
JC69I	36	-1268.5105	2609.0209	0.0000	1.0000
K2P	36	-1274.1459	2620.2918	0.0000	1.0000
SYM	40	-1271.9516	2623.9032	0.0000	1.0000
JC69	35	-1278.5475	2627.0950	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1242.8134	2731.2221	0.6884	0.6884
HKYI	40	-1244.1515	2733.8983	0.1806	0.8691
F81G	39	-1248.2347	2735.9248	0.0656	0.9346
HKYIG	41	-1242.5214	2736.7781	0.0428	0.9774
F81I	39	-1249.5167	2738.4889	0.0182	0.9956
F81IG	40	-1247.9536	2741.5025	0.0040	0.9996
HKY	39	-1253.6925	2746.8404	0.0003	0.9999
F81	38	-1259.1224	2751.5604	0.0000	0.9999
GTRG	44	-1241.0527	2752.2603	0.0000	1.0000
K2PG	37	-1262.6778	2752.5312	0.0000	1.0000
GTRI	44	-1242.3299	2754.8146	0.0000	1.0000
K2PI	37	-1263.9932	2755.1620	0.0000	1.0000
JC69G	36	-1267.2341	2755.5041	0.0000	1.0000
GTRIG	45	-1240.7837	2757.8621	0.0000	1.0000
K2PIG	38	-1262.3403	2757.9963	0.0000	1.0000
JC69I	36	-1268.5105	2758.0568	0.0000	1.0000
JC69IG	37	-1266.9201	2761.0159	0.0000	1.0000
GTR	43	-1251.7499	2767.5148	0.0000	1.0000
K2P	36	-1274.1459	2769.3276	0.0000	1.0000
JC69	35	-1278.5475	2771.9910	0.0000	1.0000
SYMG	41	-1260.1718	2772.0789	0.0000	1.0000
SYMI	41	-1261.4325	2774.6004	0.0000	1.0000
SYMIG	42	-1259.8326	2777.5403	0.0000	1.0000
SYM	40	-1271.9516	2789.4986	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15365.phylip = 1 - 464;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15365.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 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_15365.phylip = 1 - 464;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15365.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_15365.phylip = 1 - 464;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15365.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

