
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:12 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_5848.phylip" (19 taxa, 341 characters)

Minimum AIC  model: GTRG
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	-783.3228	1657.5789	0.3444	0.3444
HKYI	40	-783.9388	1658.8110	0.1860	0.5303
GTRG	44	-778.7900	1658.9583	0.1728	0.7031
HKYIG	41	-782.8714	1659.2611	0.1485	0.8516
GTRI	44	-779.5384	1660.4551	0.0817	0.9333
GTRIG	45	-778.4828	1660.9996	0.0623	0.9956
HKY	39	-790.1300	1668.6254	0.0014	0.9970
GTR	43	-785.1556	1669.0519	0.0011	0.9981
F81G	39	-790.5031	1669.3717	0.0009	0.9990
F81I	39	-791.0893	1670.5441	0.0005	0.9996
F81IG	40	-789.9831	1670.8996	0.0004	1.0000
F81	38	-797.5166	1680.8478	0.0000	1.0000
K2PG	37	-802.1786	1687.6378	0.0000	1.0000
K2PI	37	-802.6994	1688.6793	0.0000	1.0000
K2PIG	38	-801.6345	1689.0835	0.0000	1.0000
SYMG	41	-798.9370	1691.3923	0.0000	1.0000
SYMI	41	-799.5178	1692.5541	0.0000	1.0000
SYMIG	42	-798.5405	1693.2018	0.0000	1.0000
JC69G	36	-808.3568	1697.4768	0.0000	1.0000
JC69I	36	-808.8972	1698.5575	0.0000	1.0000
JC69IG	37	-807.8062	1698.8930	0.0000	1.0000
K2P	36	-809.3952	1699.5535	0.0000	1.0000
SYM	40	-805.6835	1702.3003	0.0000	1.0000
JC69	35	-815.5323	1709.3269	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-778.7900	1645.5799	0.3100	0.3100
HKYG	40	-783.3228	1646.6456	0.1820	0.4920
GTRIG	45	-778.4828	1646.9657	0.1551	0.6471
GTRI	44	-779.5384	1647.0767	0.1467	0.7938
HKYIG	41	-782.8714	1647.7427	0.1051	0.8989
HKYI	40	-783.9388	1647.8776	0.0983	0.9972
GTR	43	-785.1556	1656.3111	0.0014	0.9986
HKY	39	-790.1300	1658.2600	0.0005	0.9992
F81G	39	-790.5031	1659.0063	0.0004	0.9996
F81IG	40	-789.9831	1659.9662	0.0002	0.9998
F81I	39	-791.0893	1660.1787	0.0002	1.0000
F81	38	-797.5166	1671.0332	0.0000	1.0000
K2PG	37	-802.1786	1678.3573	0.0000	1.0000
K2PIG	38	-801.6345	1679.2689	0.0000	1.0000
K2PI	37	-802.6994	1679.3988	0.0000	1.0000
SYMG	41	-798.9370	1679.8739	0.0000	1.0000
SYMI	41	-799.5178	1681.0357	0.0000	1.0000
SYMIG	42	-798.5405	1681.0810	0.0000	1.0000
JC69G	36	-808.3568	1688.7137	0.0000	1.0000
JC69IG	37	-807.8062	1689.6125	0.0000	1.0000
JC69I	36	-808.8972	1689.7943	0.0000	1.0000
K2P	36	-809.3952	1690.7903	0.0000	1.0000
SYM	40	-805.6835	1691.3670	0.0000	1.0000
JC69	35	-815.5323	1701.0646	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-783.3228	1799.9209	0.5987	0.5987
HKYI	40	-783.9388	1801.1529	0.3233	0.9220
HKYIG	41	-782.8714	1804.8499	0.0509	0.9730
HKY	39	-790.1300	1807.7034	0.0122	0.9852
F81G	39	-790.5031	1808.4497	0.0084	0.9936
F81I	39	-791.0893	1809.6221	0.0047	0.9983
F81IG	40	-789.9831	1813.2415	0.0008	0.9991
GTRG	44	-778.7900	1814.1827	0.0005	0.9995
GTRI	44	-779.5384	1815.6795	0.0002	0.9998
F81	38	-797.5166	1816.6448	0.0001	0.9999
GTRIG	45	-778.4828	1819.4004	0.0000	0.9999
K2PG	37	-802.1786	1820.1369	0.0000	1.0000
GTR	43	-785.1556	1821.0821	0.0000	1.0000
K2PI	37	-802.6994	1821.1785	0.0000	1.0000
K2PIG	38	-801.6345	1824.8805	0.0000	1.0000
JC69G	36	-808.3568	1826.6614	0.0000	1.0000
JC69I	36	-808.8972	1827.7421	0.0000	1.0000
K2P	36	-809.3952	1828.7381	0.0000	1.0000
JC69IG	37	-807.8062	1831.3921	0.0000	1.0000
JC69	35	-815.5323	1835.1804	0.0000	1.0000
SYMG	41	-798.9370	1836.9811	0.0000	1.0000
SYMI	41	-799.5178	1838.1428	0.0000	1.0000
SYMIG	42	-798.5405	1842.0201	0.0000	1.0000
SYM	40	-805.6835	1844.6423	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/chr3_5848.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5848.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/chr3_5848.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5848.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/chr3_5848.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5848.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

