
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:16 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/chr8_4233.phylip" (19 taxa, 250 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	-767.5192	1630.7321	0.9389	0.9389
HKYG	40	-770.7604	1637.2147	0.0367	0.9756
GTRI	44	-766.2878	1639.8926	0.0096	0.9852
HKYIG	41	-770.7603	1640.0782	0.0088	0.9940
HKY	39	-774.1864	1641.2300	0.0049	0.9989
GTRG	44	-768.8049	1644.9269	0.0008	0.9997
K2PI	37	-780.7719	1648.8079	0.0001	0.9998
GTRIG	45	-769.5454	1649.3849	0.0001	0.9999
GTR	43	-772.6407	1649.6503	0.0001	1.0000
K2PG	37	-783.5024	1654.2689	0.0000	1.0000
K2PIG	38	-783.5235	1657.0945	0.0000	1.0000
SYMI	41	-780.2431	1659.0438	0.0000	1.0000
K2P	36	-789.1831	1662.8732	0.0000	1.0000
SYMG	41	-782.8893	1664.3364	0.0000	1.0000
SYMIG	42	-782.8890	1667.2273	0.0000	1.0000
SYM	40	-788.3313	1672.3565	0.0000	1.0000
F81I	39	-807.9894	1708.8359	0.0000	1.0000
F81G	39	-811.5668	1715.9908	0.0000	1.0000
F81	38	-816.0491	1722.1455	0.0000	1.0000
JC69I	36	-819.3726	1723.2522	0.0000	1.0000
F81IG	40	-814.1933	1724.0803	0.0000	1.0000
JC69G	36	-823.1970	1730.9010	0.0000	1.0000
JC69IG	37	-823.2129	1733.6899	0.0000	1.0000
JC69	35	-828.2999	1738.3755	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-767.5192	1615.0384	0.8881	0.8881
GTRI	44	-766.2878	1620.5755	0.0557	0.9438
HKYG	40	-770.7604	1621.5209	0.0347	0.9786
HKYIG	41	-770.7603	1623.5205	0.0128	0.9913
GTRG	44	-768.8049	1625.6098	0.0045	0.9958
HKY	39	-774.1864	1626.3729	0.0031	0.9989
GTRIG	45	-769.5454	1629.0908	0.0008	0.9997
GTR	43	-772.6407	1631.2814	0.0003	1.0000
K2PI	37	-780.7719	1635.5437	0.0000	1.0000
K2PG	37	-783.5024	1641.0048	0.0000	1.0000
SYMI	41	-780.2431	1642.4861	0.0000	1.0000
K2PIG	38	-783.5235	1643.0471	0.0000	1.0000
SYMG	41	-782.8893	1647.7787	0.0000	1.0000
SYMIG	42	-782.8890	1649.7780	0.0000	1.0000
K2P	36	-789.1831	1650.3661	0.0000	1.0000
SYM	40	-788.3313	1656.6627	0.0000	1.0000
F81I	39	-807.9894	1693.9788	0.0000	1.0000
F81G	39	-811.5668	1701.1337	0.0000	1.0000
F81	38	-816.0491	1708.0981	0.0000	1.0000
F81IG	40	-814.1933	1708.3866	0.0000	1.0000
JC69I	36	-819.3726	1710.7452	0.0000	1.0000
JC69G	36	-823.1970	1718.3939	0.0000	1.0000
JC69IG	37	-823.2129	1720.4258	0.0000	1.0000
JC69	35	-828.2999	1726.5998	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-767.5192	1755.8968	0.9353	0.9353
HKYG	40	-770.7604	1762.3793	0.0366	0.9719
HKY	39	-774.1864	1763.7098	0.0188	0.9907
K2PI	37	-780.7719	1765.8378	0.0065	0.9972
HKYIG	41	-770.7603	1767.9004	0.0023	0.9995
K2PG	37	-783.5024	1771.2988	0.0004	0.9999
GTRI	44	-766.2878	1775.5198	0.0001	0.9999
K2PIG	38	-783.5235	1776.8626	0.0000	1.0000
K2P	36	-789.1831	1777.1387	0.0000	1.0000
GTRG	44	-768.8049	1780.5541	0.0000	1.0000
GTR	43	-772.6407	1782.7042	0.0000	1.0000
SYMI	41	-780.2431	1786.8660	0.0000	1.0000
GTRIG	45	-769.5454	1787.5566	0.0000	1.0000
SYMG	41	-782.8893	1792.1586	0.0000	1.0000
SYM	40	-788.3313	1797.5211	0.0000	1.0000
SYMIG	42	-782.8890	1797.6794	0.0000	1.0000
F81I	39	-807.9894	1831.3158	0.0000	1.0000
JC69I	36	-819.3726	1837.5178	0.0000	1.0000
F81G	39	-811.5668	1838.4706	0.0000	1.0000
F81	38	-816.0491	1841.9136	0.0000	1.0000
JC69G	36	-823.1970	1845.1665	0.0000	1.0000
F81IG	40	-814.1933	1849.2450	0.0000	1.0000
JC69	35	-828.2999	1849.8509	0.0000	1.0000
JC69IG	37	-823.2129	1850.7198	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/chr8_4233.phylip = 1 - 250;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4233.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/chr8_4233.phylip = 1 - 250;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4233.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/chr8_4233.phylip = 1 - 250;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4233.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;


-------------------------------------------------------------
End of Output

