
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:49 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/chr7_10613.phylip" (19 taxa, 265 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	-762.9801	1620.6031	0.5318	0.5318
HKYIG	41	-762.1807	1621.8053	0.2915	0.8234
HKYI	40	-764.4078	1623.4584	0.1276	0.9509
GTRG	44	-760.2046	1626.4092	0.0292	0.9801
GTRIG	45	-759.4579	1627.8199	0.0144	0.9945
GTRI	44	-761.8848	1629.7696	0.0054	1.0000
SYMG	41	-771.8220	1641.0879	0.0000	1.0000
K2PG	37	-778.1011	1642.5898	0.0000	1.0000
SYMIG	42	-771.2163	1642.7030	0.0000	1.0000
K2PIG	38	-777.3687	1643.8525	0.0000	1.0000
SYMI	41	-773.6784	1644.8008	0.0000	1.0000
K2PI	37	-779.4770	1645.3417	0.0000	1.0000
HKY	39	-777.6842	1647.2351	0.0000	1.0000
GTR	43	-774.2856	1651.6934	0.0000	1.0000
SYM	40	-784.9966	1664.6361	0.0000	1.0000
F81G	39	-786.6912	1665.2491	0.0000	1.0000
F81IG	40	-785.9726	1666.5880	0.0000	1.0000
F81I	39	-787.7232	1667.3130	0.0000	1.0000
K2P	36	-792.7946	1669.2734	0.0000	1.0000
F81	38	-801.9297	1692.9744	0.0000	1.0000
JC69G	36	-805.1152	1693.9146	0.0000	1.0000
JC69IG	37	-804.5566	1695.5008	0.0000	1.0000
JC69I	36	-806.0607	1695.8056	0.0000	1.0000
JC69	35	-818.5447	1718.0938	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-762.9801	1605.9602	0.3795	0.3795
HKYIG	41	-762.1807	1606.3614	0.3105	0.6900
GTRG	44	-760.2046	1608.4092	0.1115	0.8016
HKYI	40	-764.4078	1608.8155	0.0910	0.8926
GTRIG	45	-759.4579	1608.9158	0.0866	0.9792
GTRI	44	-761.8848	1611.7696	0.0208	1.0000
SYMG	41	-771.8220	1625.6439	0.0000	1.0000
SYMIG	42	-771.2163	1626.4327	0.0000	1.0000
SYMI	41	-773.6784	1629.3569	0.0000	1.0000
K2PG	37	-778.1011	1630.2022	0.0000	1.0000
K2PIG	38	-777.3687	1630.7374	0.0000	1.0000
K2PI	37	-779.4770	1632.9540	0.0000	1.0000
HKY	39	-777.6842	1633.3685	0.0000	1.0000
GTR	43	-774.2856	1634.5712	0.0000	1.0000
SYM	40	-784.9966	1649.9932	0.0000	1.0000
F81G	39	-786.6912	1651.3824	0.0000	1.0000
F81IG	40	-785.9726	1651.9451	0.0000	1.0000
F81I	39	-787.7232	1653.4464	0.0000	1.0000
K2P	36	-792.7946	1657.5892	0.0000	1.0000
F81	38	-801.9297	1679.8593	0.0000	1.0000
JC69G	36	-805.1152	1682.2303	0.0000	1.0000
JC69IG	37	-804.5566	1683.1131	0.0000	1.0000
JC69I	36	-806.0607	1684.1214	0.0000	1.0000
JC69	35	-818.5447	1707.0895	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-762.9801	1749.1494	0.7255	0.7255
HKYI	40	-764.4078	1752.0047	0.1740	0.8995
HKYIG	41	-762.1807	1753.1303	0.0991	0.9986
K2PG	37	-778.1011	1762.6522	0.0008	0.9994
K2PI	37	-779.4770	1765.4040	0.0002	0.9997
GTRG	44	-760.2046	1765.9173	0.0002	0.9998
K2PIG	38	-777.3687	1766.7672	0.0001	0.9999
GTRI	44	-761.8848	1769.2777	0.0000	1.0000
GTRIG	45	-759.4579	1770.0036	0.0000	1.0000
SYMG	41	-771.8220	1772.4128	0.0000	1.0000
HKY	39	-777.6842	1772.9779	0.0000	1.0000
SYMI	41	-773.6784	1776.1258	0.0000	1.0000
SYMIG	42	-771.2163	1776.7813	0.0000	1.0000
K2P	36	-792.7946	1786.4595	0.0000	1.0000
GTR	43	-774.2856	1788.4996	0.0000	1.0000
F81G	39	-786.6912	1790.9919	0.0000	1.0000
F81I	39	-787.7232	1793.0558	0.0000	1.0000
SYM	40	-784.9966	1793.1824	0.0000	1.0000
F81IG	40	-785.9726	1795.1343	0.0000	1.0000
JC69G	36	-805.1152	1811.1006	0.0000	1.0000
JC69I	36	-806.0607	1812.9917	0.0000	1.0000
JC69IG	37	-804.5566	1815.5631	0.0000	1.0000
F81	38	-801.9297	1815.8891	0.0000	1.0000
JC69	35	-818.5447	1832.3800	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/chr7_10613.phylip = 1 - 265;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10613.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/chr7_10613.phylip = 1 - 265;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10613.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/chr7_10613.phylip = 1 - 265;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10613.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

