
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:18 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_32388.phylip" (19 taxa, 446 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	-1218.3794	2534.6342	0.3247	0.3247
GTRI	44	-1218.7770	2535.4293	0.2182	0.5429
HKYG	40	-1224.0177	2536.1342	0.1534	0.6962
HKYI	40	-1224.0823	2536.2634	0.1438	0.8400
GTRIG	45	-1218.2919	2536.9338	0.1028	0.9428
HKYIG	41	-1223.7915	2538.1077	0.0572	1.0000
K2PG	37	-1239.7024	2560.2969	0.0000	1.0000
K2PI	37	-1239.7632	2560.4185	0.0000	1.0000
K2PIG	38	-1239.5331	2562.3488	0.0000	1.0000
SYMG	41	-1237.7388	2566.0025	0.0000	1.0000
SYMI	41	-1238.1791	2566.8829	0.0000	1.0000
SYMIG	42	-1238.0916	2569.1460	0.0000	1.0000
HKY	39	-1244.0436	2573.7719	0.0000	1.0000
GTR	43	-1239.9958	2575.4045	0.0000	1.0000
F81G	39	-1248.0203	2581.7252	0.0000	1.0000
F81I	39	-1248.2480	2582.1807	0.0000	1.0000
F81IG	40	-1247.7475	2583.5938	0.0000	1.0000
K2P	36	-1258.7823	2596.0781	0.0000	1.0000
JC69G	36	-1260.7500	2600.0134	0.0000	1.0000
JC69I	36	-1260.9793	2600.4721	0.0000	1.0000
JC69IG	37	-1260.5103	2601.9127	0.0000	1.0000
SYM	40	-1256.9668	2602.0324	0.0000	1.0000
F81	38	-1266.7809	2616.8443	0.0000	1.0000
JC69	35	-1279.1784	2634.5031	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1218.3794	2524.7589	0.3938	0.3938
GTRI	44	-1218.7770	2525.5540	0.2646	0.6584
GTRIG	45	-1218.2919	2526.5838	0.1581	0.8165
HKYG	40	-1224.0177	2528.0354	0.0765	0.8930
HKYI	40	-1224.0823	2528.1647	0.0717	0.9647
HKYIG	41	-1223.7915	2529.5830	0.0353	1.0000
K2PG	37	-1239.7024	2553.4048	0.0000	1.0000
K2PI	37	-1239.7632	2553.5264	0.0000	1.0000
K2PIG	38	-1239.5331	2555.0663	0.0000	1.0000
SYMG	41	-1237.7388	2557.4777	0.0000	1.0000
SYMI	41	-1238.1791	2558.3581	0.0000	1.0000
SYMIG	42	-1238.0916	2560.1832	0.0000	1.0000
GTR	43	-1239.9958	2565.9916	0.0000	1.0000
HKY	39	-1244.0436	2566.0872	0.0000	1.0000
F81G	39	-1248.0203	2574.0405	0.0000	1.0000
F81I	39	-1248.2480	2574.4960	0.0000	1.0000
F81IG	40	-1247.7475	2575.4950	0.0000	1.0000
K2P	36	-1258.7823	2589.5647	0.0000	1.0000
JC69G	36	-1260.7500	2593.4999	0.0000	1.0000
SYM	40	-1256.9668	2593.9336	0.0000	1.0000
JC69I	36	-1260.9793	2593.9587	0.0000	1.0000
JC69IG	37	-1260.5103	2595.0206	0.0000	1.0000
F81	38	-1266.7809	2609.5618	0.0000	1.0000
JC69	35	-1279.1784	2628.3568	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1224.0177	2692.0482	0.4995	0.4995
HKYI	40	-1224.0823	2692.1774	0.4682	0.9677
HKYIG	41	-1223.7915	2697.6960	0.0297	0.9973
K2PG	37	-1239.7024	2705.1166	0.0007	0.9981
GTRG	44	-1218.3794	2705.1729	0.0007	0.9988
K2PI	37	-1239.7632	2705.2382	0.0007	0.9994
GTRI	44	-1218.7770	2705.9680	0.0005	0.9999
K2PIG	38	-1239.5331	2710.8784	0.0000	1.0000
GTRIG	45	-1218.2919	2711.0982	0.0000	1.0000
SYMG	41	-1237.7388	2725.5908	0.0000	1.0000
HKY	39	-1244.0436	2725.9997	0.0000	1.0000
SYMI	41	-1238.1791	2726.4712	0.0000	1.0000
SYMIG	42	-1238.0916	2732.3966	0.0000	1.0000
F81G	39	-1248.0203	2733.9530	0.0000	1.0000
F81I	39	-1248.2480	2734.4084	0.0000	1.0000
K2P	36	-1258.7823	2737.1762	0.0000	1.0000
F81IG	40	-1247.7475	2739.5078	0.0000	1.0000
JC69G	36	-1260.7500	2741.1114	0.0000	1.0000
JC69I	36	-1260.9793	2741.5702	0.0000	1.0000
GTR	43	-1239.9958	2742.3053	0.0000	1.0000
JC69IG	37	-1260.5103	2746.7324	0.0000	1.0000
SYM	40	-1256.9668	2757.9464	0.0000	1.0000
F81	38	-1266.7809	2765.3739	0.0000	1.0000
JC69	35	-1279.1784	2771.8680	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_32388.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32388.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/chr1_32388.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32388.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/chr1_32388.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32388.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

