
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:34 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/chr6_9069.phylip" (19 taxa, 290 characters)

Minimum AIC  model: GTRG
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	-848.1951	1789.5629	0.3993	0.3993
HKYIG	41	-847.3778	1790.6428	0.2327	0.6321
HKYI	40	-849.0773	1791.3273	0.1653	0.7973
GTRG	44	-844.1439	1792.4510	0.0942	0.8916
GTRIG	45	-843.4109	1793.7890	0.0483	0.9398
GTRI	44	-844.9997	1794.1626	0.0400	0.9799
K2PG	37	-855.8241	1796.8069	0.0107	0.9906
K2PIG	38	-855.3355	1798.4798	0.0046	0.9952
K2PI	37	-856.9723	1799.1033	0.0034	0.9986
SYMG	41	-853.1611	1802.2092	0.0007	0.9993
SYMIG	42	-852.3869	1803.3973	0.0004	0.9997
SYMI	41	-853.9438	1803.7747	0.0003	1.0000
F81G	39	-868.0633	1826.6066	0.0000	1.0000
F81I	39	-868.9933	1828.4667	0.0000	1.0000
F81IG	40	-867.7411	1828.6550	0.0000	1.0000
HKY	39	-869.6563	1829.7927	0.0000	1.0000
GTR	43	-864.6865	1830.7551	0.0000	1.0000
JC69G	36	-874.6805	1831.8907	0.0000	1.0000
JC69I	36	-875.7554	1834.0405	0.0000	1.0000
JC69IG	37	-874.5228	1834.2043	0.0000	1.0000
K2P	36	-877.7057	1837.9410	0.0000	1.0000
SYM	40	-873.7436	1840.6599	0.0000	1.0000
F81	38	-888.4876	1864.7840	0.0000	1.0000
JC69	35	-895.4892	1870.8997	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-844.1439	1776.2877	0.2300	0.2300
HKYG	40	-848.1951	1776.3902	0.2185	0.4484
HKYIG	41	-847.3778	1776.7557	0.1820	0.6304
GTRIG	45	-843.4109	1776.8218	0.1761	0.8065
GTRI	44	-844.9997	1777.9993	0.0977	0.9042
HKYI	40	-849.0773	1778.1546	0.0904	0.9946
K2PG	37	-855.8241	1785.6482	0.0021	0.9968
K2PIG	38	-855.3355	1786.6710	0.0013	0.9981
K2PI	37	-856.9723	1787.9446	0.0007	0.9987
SYMG	41	-853.1611	1788.3221	0.0006	0.9993
SYMIG	42	-852.3869	1788.7738	0.0004	0.9997
SYMI	41	-853.9438	1789.8876	0.0003	1.0000
F81G	39	-868.0633	1814.1266	0.0000	1.0000
GTR	43	-864.6865	1815.3730	0.0000	1.0000
F81IG	40	-867.7411	1815.4823	0.0000	1.0000
F81I	39	-868.9933	1815.9867	0.0000	1.0000
HKY	39	-869.6563	1817.3127	0.0000	1.0000
JC69G	36	-874.6805	1821.3611	0.0000	1.0000
JC69IG	37	-874.5228	1823.0455	0.0000	1.0000
JC69I	36	-875.7554	1823.5108	0.0000	1.0000
K2P	36	-877.7057	1827.4113	0.0000	1.0000
SYM	40	-873.7436	1827.4872	0.0000	1.0000
F81	38	-888.4876	1852.9753	0.0000	1.0000
JC69	35	-895.4892	1860.9784	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-855.8241	1921.4338	0.4859	0.4859
HKYG	40	-848.1951	1923.1854	0.2024	0.6883
K2PI	37	-856.9723	1923.7302	0.1541	0.8425
HKYI	40	-849.0773	1924.9498	0.0838	0.9262
K2PIG	38	-855.3355	1926.1265	0.0465	0.9727
HKYIG	41	-847.3778	1927.2208	0.0269	0.9997
GTRG	44	-844.1439	1937.7625	0.0001	0.9998
SYMG	41	-853.1611	1938.7872	0.0001	0.9999
GTRI	44	-844.9997	1939.4741	0.0001	0.9999
SYMI	41	-853.9438	1940.3527	0.0000	1.0000
GTRIG	45	-843.4109	1941.9664	0.0000	1.0000
SYMIG	42	-852.3869	1942.9088	0.0000	1.0000
JC69G	36	-874.6805	1953.4768	0.0000	1.0000
JC69I	36	-875.7554	1955.6265	0.0000	1.0000
F81G	39	-868.0633	1957.2519	0.0000	1.0000
JC69IG	37	-874.5228	1958.8311	0.0000	1.0000
F81I	39	-868.9933	1959.1121	0.0000	1.0000
K2P	36	-877.7057	1959.5271	0.0000	1.0000
HKY	39	-869.6563	1960.4380	0.0000	1.0000
F81IG	40	-867.7411	1962.2775	0.0000	1.0000
GTR	43	-864.6865	1973.1778	0.0000	1.0000
SYM	40	-873.7436	1974.2825	0.0000	1.0000
JC69	35	-895.4892	1989.4242	0.0000	1.0000
F81	38	-888.4876	1992.4307	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/chr6_9069.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9069.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9069.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9069.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/chr6_9069.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9069.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

