
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:09 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_28747.phylip" (19 taxa, 555 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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	-1356.6660	2799.7133	0.4163	0.4163
HKYG	40	-1356.6789	2799.7391	0.4110	0.8273
HKYIG	41	-1356.6809	2802.0752	0.1278	0.9551
GTRI	44	-1355.0327	2805.8301	0.0196	0.9747
GTRG	44	-1355.0413	2805.8472	0.0194	0.9941
GTRIG	45	-1355.0411	2808.2158	0.0059	1.0000
HKY	39	-1374.2693	2832.5968	0.0000	1.0000
GTR	43	-1372.7765	2838.9582	0.0000	1.0000
K2PI	37	-1380.2790	2839.9970	0.0000	1.0000
K2PG	37	-1380.2799	2839.9988	0.0000	1.0000
K2PIG	38	-1380.2798	2842.3038	0.0000	1.0000
SYMI	41	-1379.7717	2848.2568	0.0000	1.0000
SYMG	41	-1379.7807	2848.2749	0.0000	1.0000
SYMIG	42	-1379.7815	2850.6177	0.0000	1.0000
F81I	39	-1384.9313	2853.9209	0.0000	1.0000
F81G	39	-1385.0114	2854.0811	0.0000	1.0000
F81IG	40	-1385.0114	2856.4041	0.0000	1.0000
K2P	36	-1397.9420	2873.0268	0.0000	1.0000
SYM	40	-1397.3784	2881.1382	0.0000	1.0000
F81	38	-1402.0888	2885.9218	0.0000	1.0000
JC69I	36	-1405.4859	2888.1146	0.0000	1.0000
JC69G	36	-1405.5547	2888.2522	0.0000	1.0000
JC69IG	37	-1405.5546	2890.5482	0.0000	1.0000
JC69	35	-1422.8260	2920.5074	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1356.6660	2793.3320	0.3890	0.3890
HKYG	40	-1356.6789	2793.3578	0.3840	0.7730
HKYIG	41	-1356.6809	2795.3617	0.1410	0.9140
GTRI	44	-1355.0327	2798.0654	0.0365	0.9505
GTRG	44	-1355.0413	2798.0825	0.0362	0.9867
GTRIG	45	-1355.0411	2800.0822	0.0133	1.0000
HKY	39	-1374.2693	2826.5386	0.0000	1.0000
GTR	43	-1372.7765	2831.5531	0.0000	1.0000
K2PI	37	-1380.2790	2834.5579	0.0000	1.0000
K2PG	37	-1380.2799	2834.5597	0.0000	1.0000
K2PIG	38	-1380.2798	2836.5596	0.0000	1.0000
SYMI	41	-1379.7717	2841.5434	0.0000	1.0000
SYMG	41	-1379.7807	2841.5615	0.0000	1.0000
SYMIG	42	-1379.7815	2843.5630	0.0000	1.0000
F81I	39	-1384.9313	2847.8626	0.0000	1.0000
F81G	39	-1385.0114	2848.0228	0.0000	1.0000
F81IG	40	-1385.0114	2850.0228	0.0000	1.0000
K2P	36	-1397.9420	2867.8840	0.0000	1.0000
SYM	40	-1397.3784	2874.7569	0.0000	1.0000
F81	38	-1402.0888	2880.1777	0.0000	1.0000
JC69I	36	-1405.4859	2882.9717	0.0000	1.0000
JC69G	36	-1405.5547	2883.1093	0.0000	1.0000
JC69IG	37	-1405.5546	2885.1092	0.0000	1.0000
JC69	35	-1422.8260	2915.6519	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1356.6660	2966.0907	0.4928	0.4928
HKYG	40	-1356.6789	2966.1165	0.4865	0.9794
HKYIG	41	-1356.6809	2972.4394	0.0206	1.0000
GTRI	44	-1355.0327	2988.1000	0.0000	1.0000
GTRG	44	-1355.0413	2988.1171	0.0000	1.0000
K2PI	37	-1380.2790	2994.3597	0.0000	1.0000
K2PG	37	-1380.2799	2994.3616	0.0000	1.0000
GTRIG	45	-1355.0411	2994.4358	0.0000	1.0000
HKY	39	-1374.2693	2994.9783	0.0000	1.0000
K2PIG	38	-1380.2798	3000.6804	0.0000	1.0000
F81I	39	-1384.9313	3016.3024	0.0000	1.0000
F81G	39	-1385.0114	3016.4626	0.0000	1.0000
GTR	43	-1372.7765	3017.2687	0.0000	1.0000
SYMI	41	-1379.7717	3018.6211	0.0000	1.0000
SYMG	41	-1379.7807	3018.6392	0.0000	1.0000
F81IG	40	-1385.0114	3022.7815	0.0000	1.0000
K2P	36	-1397.9420	3023.3668	0.0000	1.0000
SYMIG	42	-1379.7815	3024.9596	0.0000	1.0000
JC69I	36	-1405.4859	3038.4546	0.0000	1.0000
JC69G	36	-1405.5547	3038.5922	0.0000	1.0000
F81	38	-1402.0888	3044.2984	0.0000	1.0000
JC69IG	37	-1405.5546	3044.9110	0.0000	1.0000
SYM	40	-1397.3784	3047.5156	0.0000	1.0000
JC69	35	-1422.8260	3066.8158	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.phylip = 1 - 555;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.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 AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.phylip = 1 - 555;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.phylip = 1 - 555;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28747.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;


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End of Output

