
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:46 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/chr3_25156.phylip" (19 taxa, 248 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-758.9283	1613.7020	0.4573	0.4573
HKYI	40	-759.6884	1615.2222	0.2138	0.6711
HKYIG	41	-758.5647	1615.8479	0.1564	0.8275
GTRG	44	-755.3738	1618.2551	0.0469	0.8744
K2PG	37	-765.5202	1618.4309	0.0430	0.9174
GTRI	44	-756.0443	1619.5960	0.0240	0.9414
K2PI	37	-766.3855	1620.1615	0.0181	0.9595
K2PIG	38	-765.0730	1620.3278	0.0166	0.9761
GTRIG	45	-755.1785	1620.8520	0.0128	0.9890
SYMG	41	-761.8101	1622.3386	0.0061	0.9950
SYMI	41	-762.4721	1623.6626	0.0031	0.9982
SYMIG	42	-761.5731	1624.7656	0.0018	1.0000
HKY	39	-777.5588	1648.1177	0.0000	1.0000
GTR	43	-772.8817	1650.3125	0.0000	1.0000
K2P	36	-784.1329	1652.8915	0.0000	1.0000
F81G	39	-780.5822	1654.1644	0.0000	1.0000
SYM	40	-779.6617	1655.1687	0.0000	1.0000
F81I	39	-781.3451	1655.6903	0.0000	1.0000
JC69G	36	-785.7678	1656.1612	0.0000	1.0000
F81IG	40	-780.2655	1656.3764	0.0000	1.0000
JC69I	36	-786.5770	1657.7796	0.0000	1.0000
JC69IG	37	-785.4112	1658.2130	0.0000	1.0000
F81	38	-798.3251	1686.8319	0.0000	1.0000
JC69	35	-803.6183	1689.1235	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-758.9283	1597.8566	0.2988	0.2988
GTRG	44	-755.3738	1598.7477	0.1913	0.4901
HKYIG	41	-758.5647	1599.1294	0.1581	0.6482
HKYI	40	-759.6884	1599.3768	0.1397	0.7879
GTRI	44	-756.0443	1600.0886	0.0979	0.8858
GTRIG	45	-755.1785	1600.3570	0.0856	0.9714
K2PG	37	-765.5202	1605.0404	0.0082	0.9796
SYMG	41	-761.8101	1605.6202	0.0062	0.9858
K2PIG	38	-765.0730	1606.1460	0.0047	0.9905
K2PI	37	-766.3855	1606.7711	0.0035	0.9940
SYMI	41	-762.4721	1606.9441	0.0032	0.9971
SYMIG	42	-761.5731	1607.1461	0.0029	1.0000
GTR	43	-772.8817	1631.7635	0.0000	1.0000
HKY	39	-777.5588	1633.1177	0.0000	1.0000
F81G	39	-780.5822	1639.1644	0.0000	1.0000
SYM	40	-779.6617	1639.3233	0.0000	1.0000
K2P	36	-784.1329	1640.2659	0.0000	1.0000
F81IG	40	-780.2655	1640.5310	0.0000	1.0000
F81I	39	-781.3451	1640.6903	0.0000	1.0000
JC69G	36	-785.7678	1643.5356	0.0000	1.0000
JC69IG	37	-785.4112	1644.8225	0.0000	1.0000
JC69I	36	-786.5770	1645.1540	0.0000	1.0000
F81	38	-798.3251	1672.6501	0.0000	1.0000
JC69	35	-803.6183	1677.2367	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-765.5202	1735.0373	0.5517	0.5517
K2PI	37	-766.3855	1736.7679	0.2322	0.7839
HKYG	40	-758.9283	1738.3938	0.1030	0.8870
K2PIG	38	-765.0730	1739.6563	0.0548	0.9417
HKYI	40	-759.6884	1739.9140	0.0482	0.9899
HKYIG	41	-758.5647	1743.1800	0.0094	0.9993
SYMG	41	-761.8101	1749.6707	0.0004	0.9997
SYMI	41	-762.4721	1750.9947	0.0002	0.9999
GTRG	44	-755.3738	1753.3385	0.0001	0.9999
GTRI	44	-756.0443	1754.6795	0.0000	1.0000
SYMIG	42	-761.5731	1754.7101	0.0000	1.0000
GTRIG	45	-755.1785	1758.4613	0.0000	1.0000
K2P	36	-784.1329	1766.7493	0.0000	1.0000
JC69G	36	-785.7678	1770.0190	0.0000	1.0000
HKY	39	-777.5588	1770.1414	0.0000	1.0000
JC69I	36	-786.5770	1771.6375	0.0000	1.0000
JC69IG	37	-785.4112	1774.8193	0.0000	1.0000
F81G	39	-780.5822	1776.1882	0.0000	1.0000
F81I	39	-781.3451	1777.7140	0.0000	1.0000
SYM	40	-779.6617	1779.8605	0.0000	1.0000
F81IG	40	-780.2655	1781.0681	0.0000	1.0000
GTR	43	-772.8817	1782.8409	0.0000	1.0000
JC69	35	-803.6183	1800.2067	0.0000	1.0000
F81	38	-798.3251	1806.1604	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/chr3_25156.phylip = 1 - 248;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25156.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/chr3_25156.phylip = 1 - 248;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25156.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25156.phylip = 1 - 248;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_25156.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

