
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:43 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/chr2_18637.phylip" (19 taxa, 272 characters)

Minimum AIC  model: GTRG
Minimum AICc model: K2PG
Minimum BIC  model: K2PG


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
K2PG	37	-808.1087	1702.2345	0.2000	0.2000
K2PI	37	-808.4065	1702.8302	0.1485	0.3485
GTRG	44	-798.7467	1702.9383	0.1407	0.4892
GTRI	44	-799.0515	1703.5480	0.1037	0.5929
SYMG	41	-803.5172	1704.0083	0.0824	0.6753
HKYG	40	-805.0635	1704.3261	0.0703	0.7456
SYMI	41	-803.7592	1704.4923	0.0647	0.8103
K2PIG	38	-807.9979	1704.7169	0.0578	0.8681
HKYI	40	-805.2898	1704.7788	0.0561	0.9242
GTRIG	45	-798.6693	1705.6572	0.0361	0.9603
SYMIG	42	-803.4666	1706.7061	0.0214	0.9817
HKYIG	41	-805.0206	1707.0152	0.0183	1.0000
SYM	40	-821.2255	1736.6501	0.0000	1.0000
K2P	36	-829.2532	1741.8426	0.0000	1.0000
HKY	39	-826.1295	1743.7072	0.0000	1.0000
GTR	43	-820.9968	1744.5901	0.0000	1.0000
JC69I	36	-840.3104	1763.9569	0.0000	1.0000
JC69G	36	-840.3854	1764.1070	0.0000	1.0000
F81I	39	-837.9634	1767.3751	0.0000	1.0000
F81G	39	-838.0589	1767.5660	0.0000	1.0000
JC69IG	37	-843.3635	1772.7441	0.0000	1.0000
F81IG	40	-840.8213	1775.8417	0.0000	1.0000
JC69	35	-857.8113	1796.3005	0.0000	1.0000
F81	38	-855.5539	1799.8289	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-798.7467	1685.4934	0.3422	0.3422
GTRI	44	-799.0515	1686.1030	0.2523	0.5944
GTRIG	45	-798.6693	1687.3386	0.1360	0.7304
SYMG	41	-803.5172	1689.0343	0.0583	0.7887
SYMI	41	-803.7592	1689.5183	0.0457	0.8344
HKYG	40	-805.0635	1690.1270	0.0337	0.8682
K2PG	37	-808.1087	1690.2174	0.0322	0.9004
HKYI	40	-805.2898	1690.5797	0.0269	0.9273
K2PI	37	-808.4065	1690.8131	0.0239	0.9513
SYMIG	42	-803.4666	1690.9332	0.0225	0.9738
K2PIG	38	-807.9979	1691.9959	0.0133	0.9870
HKYIG	41	-805.0206	1692.0413	0.0130	1.0000
SYM	40	-821.2255	1722.4510	0.0000	1.0000
GTR	43	-820.9968	1727.9936	0.0000	1.0000
HKY	39	-826.1295	1730.2589	0.0000	1.0000
K2P	36	-829.2532	1730.5064	0.0000	1.0000
JC69I	36	-840.3104	1752.6207	0.0000	1.0000
JC69G	36	-840.3854	1752.7709	0.0000	1.0000
F81I	39	-837.9634	1753.9268	0.0000	1.0000
F81G	39	-838.0589	1754.1177	0.0000	1.0000
JC69IG	37	-843.3635	1760.7270	0.0000	1.0000
F81IG	40	-840.8213	1761.6426	0.0000	1.0000
JC69	35	-857.8113	1785.6225	0.0000	1.0000
F81	38	-855.5539	1787.1079	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-808.1087	1823.6320	0.5490	0.5490
K2PI	37	-808.4065	1824.2278	0.4076	0.9566
K2PIG	38	-807.9979	1829.0164	0.0372	0.9938
HKYG	40	-805.0635	1834.3590	0.0026	0.9964
HKYI	40	-805.2898	1834.8118	0.0021	0.9984
SYMG	41	-803.5172	1836.8722	0.0007	0.9992
SYMI	41	-803.7592	1837.3562	0.0006	0.9998
HKYIG	41	-805.0206	1839.8792	0.0002	0.9999
SYMIG	42	-803.4666	1842.3769	0.0000	1.0000
GTRG	44	-798.7467	1844.1487	0.0000	1.0000
GTRI	44	-799.0515	1844.7583	0.0000	1.0000
GTRIG	45	-798.6693	1849.5997	0.0000	1.0000
K2P	36	-829.2532	1860.3153	0.0000	1.0000
SYM	40	-821.2255	1866.6831	0.0000	1.0000
HKY	39	-826.1295	1870.8852	0.0000	1.0000
JC69I	36	-840.3104	1882.4296	0.0000	1.0000
JC69G	36	-840.3854	1882.5797	0.0000	1.0000
GTR	43	-820.9968	1883.0431	0.0000	1.0000
JC69IG	37	-843.3635	1894.1417	0.0000	1.0000
F81I	39	-837.9634	1894.5531	0.0000	1.0000
F81G	39	-838.0589	1894.7440	0.0000	1.0000
F81IG	40	-840.8213	1905.8746	0.0000	1.0000
JC69	35	-857.8113	1911.8256	0.0000	1.0000
F81	38	-855.5539	1924.1284	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/chr2_18637.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18637.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18637.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18637.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18637.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18637.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

