
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr5_11231.phylip" (19 taxa, 283 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2P


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	-793.5227	1680.5991	0.3529	0.3529
HKYI	40	-793.8964	1681.3466	0.2429	0.5958
HKY	39	-795.5998	1682.0391	0.1718	0.7676
HKYIG	41	-793.5220	1683.3345	0.0899	0.8575
K2PG	37	-800.1394	1685.7563	0.0268	0.8843
GTRG	44	-790.7728	1686.1842	0.0216	0.9059
K2P	36	-801.8495	1686.5283	0.0182	0.9241
K2PI	37	-800.5390	1686.5556	0.0180	0.9421
GTRI	44	-791.0734	1686.7856	0.0160	0.9581
GTR	43	-792.6713	1687.1752	0.0132	0.9712
K2PIG	38	-800.1453	1688.4381	0.0070	0.9782
SYMG	41	-796.2454	1688.7813	0.0059	0.9841
GTRIG	45	-790.7720	1689.0123	0.0053	0.9894
SYM	40	-797.8130	1689.1796	0.0048	0.9942
SYMI	41	-796.5702	1689.4308	0.0043	0.9985
SYMIG	42	-796.2504	1691.5508	0.0015	1.0000
F81G	39	-806.0943	1703.0281	0.0000	1.0000
F81I	39	-806.4185	1703.6766	0.0000	1.0000
F81	38	-807.7960	1703.7396	0.0000	1.0000
F81IG	40	-806.0978	1705.7493	0.0000	1.0000
JC69G	36	-811.7644	1706.3580	0.0000	1.0000
JC69	35	-813.2862	1706.7749	0.0000	1.0000
JC69I	36	-812.0986	1707.0265	0.0000	1.0000
JC69IG	37	-811.7704	1709.0183	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-793.5227	1667.0454	0.3077	0.3077
HKYI	40	-793.8964	1667.7928	0.2118	0.5195
HKYIG	41	-793.5220	1669.0441	0.1133	0.6328
HKY	39	-795.5998	1669.1996	0.1048	0.7376
GTRG	44	-790.7728	1669.5455	0.0882	0.8257
GTRI	44	-791.0734	1670.1469	0.0653	0.8910
GTR	43	-792.6713	1671.3425	0.0359	0.9269
GTRIG	45	-790.7720	1671.5440	0.0325	0.9593
K2PG	37	-800.1394	1674.2787	0.0083	0.9676
SYMG	41	-796.2454	1674.4908	0.0074	0.9750
K2PI	37	-800.5390	1675.0780	0.0055	0.9806
SYMI	41	-796.5702	1675.1403	0.0054	0.9860
SYM	40	-797.8130	1675.6259	0.0042	0.9902
K2P	36	-801.8495	1675.6990	0.0041	0.9942
K2PIG	38	-800.1453	1676.2906	0.0030	0.9973
SYMIG	42	-796.2504	1676.5008	0.0027	1.0000
F81G	39	-806.0943	1690.1886	0.0000	1.0000
F81I	39	-806.4185	1690.8371	0.0000	1.0000
F81	38	-807.7960	1691.5921	0.0000	1.0000
F81IG	40	-806.0978	1692.1955	0.0000	1.0000
JC69G	36	-811.7644	1695.5287	0.0000	1.0000
JC69I	36	-812.0986	1696.1973	0.0000	1.0000
JC69	35	-813.2862	1696.5724	0.0000	1.0000
JC69IG	37	-811.7704	1697.5407	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-801.8495	1806.9351	0.5653	0.5653
K2PG	37	-800.1394	1809.1603	0.1858	0.7511
K2PI	37	-800.5390	1809.9596	0.1246	0.8758
HKY	39	-795.5998	1811.3720	0.0615	0.9372
HKYG	40	-793.5227	1812.8633	0.0292	0.9664
HKYI	40	-793.8964	1813.6107	0.0201	0.9865
K2PIG	38	-800.1453	1814.8175	0.0110	0.9975
HKYIG	41	-793.5220	1818.5074	0.0017	0.9992
SYM	40	-797.8130	1821.4438	0.0004	0.9996
SYMG	41	-796.2454	1823.9541	0.0001	0.9997
JC69	35	-813.2862	1824.1631	0.0001	0.9998
SYMI	41	-796.5702	1824.6036	0.0001	0.9999
JC69G	36	-811.7644	1826.7648	0.0000	0.9999
JC69I	36	-812.0986	1827.4334	0.0000	1.0000
GTR	43	-792.6713	1828.0968	0.0000	1.0000
SYMIG	42	-796.2504	1829.6096	0.0000	1.0000
GTRG	44	-790.7728	1829.9452	0.0000	1.0000
F81	38	-807.7960	1830.1191	0.0000	1.0000
GTRI	44	-791.0734	1830.5466	0.0000	1.0000
F81G	39	-806.0943	1832.3610	0.0000	1.0000
JC69IG	37	-811.7704	1832.4223	0.0000	1.0000
F81I	39	-806.4185	1833.0095	0.0000	1.0000
GTRIG	45	-790.7720	1835.5891	0.0000	1.0000
F81IG	40	-806.0978	1838.0134	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/chr5_11231.phylip = 1 - 283;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11231.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/chr5_11231.phylip = 1 - 283;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11231.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 (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11231.phylip = 1 - 283;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11231.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

