
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:10 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_661.phylip" (19 taxa, 236 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


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	-796.5083	1689.8372	0.4860	0.4860
HKYI	40	-797.2903	1691.4010	0.2224	0.7084
HKYIG	41	-796.5139	1692.7804	0.1116	0.8200
HKY	39	-799.5639	1693.0461	0.0977	0.9177
GTRG	44	-792.9349	1694.6028	0.0449	0.9625
GTRI	44	-793.6712	1696.0753	0.0215	0.9840
GTRIG	45	-792.9403	1697.6700	0.0097	0.9937
GTR	43	-796.4088	1698.5259	0.0063	1.0000
K2PG	37	-813.7756	1715.7533	0.0000	1.0000
K2PI	37	-814.3718	1716.9456	0.0000	1.0000
K2PIG	38	-813.7828	1718.6114	0.0000	1.0000
K2P	36	-816.8170	1719.0210	0.0000	1.0000
F81G	39	-813.6734	1721.2651	0.0000	1.0000
F81I	39	-814.4064	1722.7313	0.0000	1.0000
F81IG	40	-813.6786	1724.1778	0.0000	1.0000
F81	38	-816.6026	1724.2509	0.0000	1.0000
SYMG	41	-812.8247	1725.4019	0.0000	1.0000
SYMI	41	-813.5591	1726.8707	0.0000	1.0000
SYM	40	-815.7738	1728.3681	0.0000	1.0000
SYMIG	42	-812.8298	1728.3747	0.0000	1.0000
JC69G	36	-828.4240	1742.2350	0.0000	1.0000
JC69I	36	-829.0883	1743.5635	0.0000	1.0000
JC69IG	37	-828.4290	1745.0601	0.0000	1.0000
JC69	35	-831.3611	1745.3222	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-796.5083	1673.0167	0.3115	0.3115
GTRG	44	-792.9349	1673.8699	0.2033	0.5148
HKYI	40	-797.2903	1674.5805	0.1425	0.6573
HKYIG	41	-796.5139	1675.0278	0.1139	0.7712
GTRI	44	-793.6712	1675.3423	0.0974	0.8686
GTRIG	45	-792.9403	1675.8805	0.0744	0.9430
HKY	39	-799.5639	1677.1277	0.0399	0.9829
GTR	43	-796.4088	1678.8175	0.0171	1.0000
K2PG	37	-813.7756	1701.5512	0.0000	1.0000
K2PI	37	-814.3718	1702.7436	0.0000	1.0000
K2PIG	38	-813.7828	1703.5657	0.0000	1.0000
F81G	39	-813.6734	1705.3468	0.0000	1.0000
K2P	36	-816.8170	1705.6340	0.0000	1.0000
F81I	39	-814.4064	1706.8129	0.0000	1.0000
F81IG	40	-813.6786	1707.3572	0.0000	1.0000
SYMG	41	-812.8247	1707.6494	0.0000	1.0000
SYMI	41	-813.5591	1709.1181	0.0000	1.0000
F81	38	-816.6026	1709.2052	0.0000	1.0000
SYMIG	42	-812.8298	1709.6597	0.0000	1.0000
SYM	40	-815.7738	1711.5476	0.0000	1.0000
JC69G	36	-828.4240	1728.8481	0.0000	1.0000
JC69I	36	-829.0883	1730.1765	0.0000	1.0000
JC69IG	37	-828.4290	1730.8581	0.0000	1.0000
JC69	35	-831.3611	1732.7222	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-796.5083	1811.5700	0.4450	0.4450
HKY	39	-799.5639	1812.2172	0.3219	0.7669
HKYI	40	-797.2903	1813.1338	0.2036	0.9705
HKYIG	41	-796.5139	1817.0449	0.0288	0.9993
GTRG	44	-792.9349	1826.2785	0.0003	0.9996
GTRI	44	-793.6712	1827.7509	0.0001	0.9997
GTR	43	-796.4088	1827.7623	0.0001	0.9999
K2PG	37	-813.7756	1829.7130	0.0001	0.9999
K2P	36	-816.8170	1830.3320	0.0000	0.9999
K2PI	37	-814.3718	1830.9054	0.0000	1.0000
GTRIG	45	-792.9403	1831.7530	0.0000	1.0000
K2PIG	38	-813.7828	1835.1913	0.0000	1.0000
F81G	39	-813.6734	1840.4362	0.0000	1.0000
F81	38	-816.6026	1840.8308	0.0000	1.0000
F81I	39	-814.4064	1841.9023	0.0000	1.0000
F81IG	40	-813.6786	1845.9105	0.0000	1.0000
SYMG	41	-812.8247	1849.6665	0.0000	1.0000
SYM	40	-815.7738	1850.1009	0.0000	1.0000
SYMI	41	-813.5591	1851.1352	0.0000	1.0000
JC69G	36	-828.4240	1853.5460	0.0000	1.0000
JC69	35	-831.3611	1853.9563	0.0000	1.0000
JC69I	36	-829.0883	1854.8745	0.0000	1.0000
SYMIG	42	-812.8298	1855.1406	0.0000	1.0000
JC69IG	37	-828.4290	1859.0199	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/chr8_661.phylip = 1 - 236;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_661.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/chr8_661.phylip = 1 - 236;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_661.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_661.phylip = 1 - 236;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_661.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;


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End of Output

