
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:03 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/chr10_4414.phylip" (19 taxa, 358 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	-764.0259	1618.3988	0.4300	0.4300
HKYG	40	-764.0390	1618.4250	0.4244	0.8544
HKYIG	41	-764.0388	1620.9763	0.1185	0.9729
GTRI	44	-762.5810	1625.8137	0.0106	0.9835
GTRG	44	-762.5843	1625.8203	0.0105	0.9940
HKY	39	-770.2190	1628.2492	0.0031	0.9971
GTRIG	45	-762.5852	1628.4397	0.0028	0.9999
GTR	43	-768.9323	1635.9155	0.0001	1.0000
F81I	39	-780.1821	1648.1756	0.0000	1.0000
F81G	39	-780.1888	1648.1888	0.0000	1.0000
F81IG	40	-780.2155	1650.7779	0.0000	1.0000
F81	38	-785.9349	1657.1613	0.0000	1.0000
K2PI	37	-790.1380	1663.0634	0.0000	1.0000
K2PG	37	-790.1456	1663.0787	0.0000	1.0000
K2PIG	38	-790.1458	1665.5832	0.0000	1.0000
SYMI	41	-789.9089	1672.7166	0.0000	1.0000
K2P	36	-796.2157	1672.7305	0.0000	1.0000
SYMG	41	-789.9185	1672.7357	0.0000	1.0000
SYMIG	42	-789.9182	1675.3032	0.0000	1.0000
SYM	40	-795.9200	1682.1871	0.0000	1.0000
JC69I	36	-803.5784	1687.4559	0.0000	1.0000
JC69G	36	-803.5824	1687.4640	0.0000	1.0000
JC69IG	37	-803.6034	1689.9943	0.0000	1.0000
JC69	35	-809.4417	1696.7094	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-764.0259	1608.0518	0.3938	0.3938
HKYG	40	-764.0390	1608.0780	0.3886	0.7824
HKYIG	41	-764.0388	1610.0776	0.1430	0.9254
GTRI	44	-762.5810	1613.1620	0.0306	0.9560
GTRG	44	-762.5843	1613.1686	0.0305	0.9865
GTRIG	45	-762.5852	1615.1705	0.0112	0.9977
HKY	39	-770.2190	1618.4379	0.0022	0.9999
GTR	43	-768.9323	1623.8645	0.0001	1.0000
F81I	39	-780.1821	1638.3643	0.0000	1.0000
F81G	39	-780.1888	1638.3775	0.0000	1.0000
F81IG	40	-780.2155	1640.4309	0.0000	1.0000
F81	38	-785.9349	1647.8698	0.0000	1.0000
K2PI	37	-790.1380	1654.2759	0.0000	1.0000
K2PG	37	-790.1456	1654.2912	0.0000	1.0000
K2PIG	38	-790.1458	1656.2917	0.0000	1.0000
SYMI	41	-789.9089	1661.8178	0.0000	1.0000
SYMG	41	-789.9185	1661.8369	0.0000	1.0000
SYMIG	42	-789.9182	1663.8365	0.0000	1.0000
K2P	36	-796.2157	1664.4314	0.0000	1.0000
SYM	40	-795.9200	1671.8401	0.0000	1.0000
JC69I	36	-803.5784	1679.1569	0.0000	1.0000
JC69G	36	-803.5824	1679.1649	0.0000	1.0000
JC69IG	37	-803.6034	1681.2068	0.0000	1.0000
JC69	35	-809.4417	1688.8834	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-764.0259	1763.2731	0.4813	0.4813
HKYG	40	-764.0390	1763.2993	0.4750	0.9562
HKYIG	41	-764.0388	1769.1794	0.0251	0.9814
HKY	39	-770.2190	1769.7787	0.0186	1.0000
GTRI	44	-762.5810	1783.9054	0.0000	1.0000
GTRG	44	-762.5843	1783.9120	0.0000	1.0000
F81I	39	-780.1821	1789.7050	0.0000	1.0000
F81G	39	-780.1888	1789.7183	0.0000	1.0000
GTRIG	45	-762.5852	1789.7945	0.0000	1.0000
GTR	43	-768.9323	1790.7274	0.0000	1.0000
F81	38	-785.9349	1795.3301	0.0000	1.0000
F81IG	40	-780.2155	1795.6522	0.0000	1.0000
K2PI	37	-790.1380	1797.8556	0.0000	1.0000
K2PG	37	-790.1456	1797.8709	0.0000	1.0000
K2PIG	38	-790.1458	1803.7519	0.0000	1.0000
K2P	36	-796.2157	1804.1306	0.0000	1.0000
JC69I	36	-803.5784	1818.8560	0.0000	1.0000
JC69G	36	-803.5824	1818.8641	0.0000	1.0000
SYMI	41	-789.9089	1820.9197	0.0000	1.0000
SYMG	41	-789.9185	1820.9388	0.0000	1.0000
JC69	35	-809.4417	1824.7020	0.0000	1.0000
JC69IG	37	-803.6034	1824.7866	0.0000	1.0000
SYMIG	42	-789.9182	1826.8189	0.0000	1.0000
SYM	40	-795.9200	1827.0614	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/chr10_4414.phylip = 1 - 358;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4414.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/chr10_4414.phylip = 1 - 358;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4414.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/chr10_4414.phylip = 1 - 358;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4414.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

