
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:52 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_17666.phylip" (19 taxa, 211 characters)

Minimum AIC  model: K2PG
Minimum AICc model: K2PG
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
K2PG	37	-785.7758	1661.8059	0.4823	0.4823
K2PI	37	-786.4541	1663.1626	0.2447	0.7270
K2PIG	38	-785.7819	1664.7964	0.1081	0.8352
HKYG	40	-782.9667	1665.2275	0.0872	0.9223
HKYI	40	-783.7976	1666.8892	0.0380	0.9603
HKYIG	41	-782.9723	1668.3233	0.0185	0.9789
K2P	36	-791.5628	1670.4360	0.0064	0.9853
SYMG	41	-784.0526	1670.4838	0.0063	0.9916
SYMI	41	-784.7366	1671.8519	0.0032	0.9948
GTRI	44	-780.1612	1672.1778	0.0027	0.9975
SYMIG	42	-784.0522	1673.6045	0.0013	0.9988
GTRG	44	-781.2685	1674.3923	0.0009	0.9997
GTRIG	45	-781.2683	1677.6275	0.0002	0.9999
SYM	40	-790.0953	1679.4846	0.0001	0.9999
HKY	39	-791.6744	1679.5944	0.0001	1.0000
GTR	43	-787.8279	1684.3144	0.0000	1.0000
JC69G	36	-804.4514	1696.2132	0.0000	1.0000
JC69I	36	-805.1166	1697.5435	0.0000	1.0000
JC69IG	37	-804.4511	1699.1565	0.0000	1.0000
F81G	39	-801.6459	1699.5374	0.0000	1.0000
F81I	39	-802.3247	1700.8950	0.0000	1.0000
F81IG	40	-801.6469	1702.5879	0.0000	1.0000
JC69	35	-810.3585	1705.1169	0.0000	1.0000
F81	38	-809.8282	1712.8889	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
K2PG	37	-785.7758	1645.5516	0.2547	0.2547
HKYG	40	-782.9667	1645.9334	0.2104	0.4651
K2PI	37	-786.4541	1646.9083	0.1292	0.5943
K2PIG	38	-785.7819	1647.5639	0.0931	0.6874
HKYI	40	-783.7976	1647.5951	0.0917	0.7791
HKYIG	41	-782.9723	1647.9446	0.0770	0.8561
GTRI	44	-780.1612	1648.3224	0.0637	0.9198
SYMG	41	-784.0526	1650.1051	0.0261	0.9459
GTRG	44	-781.2685	1650.5369	0.0211	0.9670
SYMI	41	-784.7366	1651.4732	0.0132	0.9802
SYMIG	42	-784.0522	1652.1045	0.0096	0.9898
GTRIG	45	-781.2683	1652.5366	0.0077	0.9975
K2P	36	-791.5628	1655.1257	0.0021	0.9997
SYM	40	-790.0953	1660.1905	0.0002	0.9998
HKY	39	-791.6744	1661.3487	0.0001	0.9999
GTR	43	-787.8279	1661.6558	0.0001	1.0000
JC69G	36	-804.4514	1680.9028	0.0000	1.0000
F81G	39	-801.6459	1681.2918	0.0000	1.0000
JC69I	36	-805.1166	1682.2331	0.0000	1.0000
F81I	39	-802.3247	1682.6494	0.0000	1.0000
JC69IG	37	-804.4511	1682.9021	0.0000	1.0000
F81IG	40	-801.6469	1683.2938	0.0000	1.0000
JC69	35	-810.3585	1690.7169	0.0000	1.0000
F81	38	-809.8282	1695.6564	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-785.7758	1769.5703	0.6140	0.6140
K2PI	37	-786.4541	1770.9270	0.3116	0.9255
K2PIG	38	-785.7819	1774.9345	0.0420	0.9675
K2P	36	-791.5628	1775.7926	0.0274	0.9949
HKYG	40	-782.9667	1780.0077	0.0033	0.9982
HKYI	40	-783.7976	1781.6694	0.0014	0.9996
HKYIG	41	-782.9723	1785.3708	0.0002	0.9999
SYMG	41	-784.0526	1787.5313	0.0001	0.9999
SYMI	41	-784.7366	1788.8994	0.0000	1.0000
HKY	39	-791.6744	1792.0712	0.0000	1.0000
SYMIG	42	-784.0522	1792.8825	0.0000	1.0000
SYM	40	-790.0953	1794.2648	0.0000	1.0000
GTRI	44	-780.1612	1795.8042	0.0000	1.0000
GTRG	44	-781.2685	1798.0187	0.0000	1.0000
JC69G	36	-804.4514	1801.5697	0.0000	1.0000
JC69I	36	-805.1166	1802.9000	0.0000	1.0000
GTRIG	45	-781.2683	1803.3702	0.0000	1.0000
GTR	43	-787.8279	1805.7857	0.0000	1.0000
JC69IG	37	-804.4511	1806.9209	0.0000	1.0000
JC69	35	-810.3585	1808.0320	0.0000	1.0000
F81G	39	-801.6459	1812.0142	0.0000	1.0000
F81I	39	-802.3247	1813.3718	0.0000	1.0000
F81IG	40	-801.6469	1817.3681	0.0000	1.0000
F81	38	-809.8282	1823.0270	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17666.phylip = 1 - 211;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17666.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;


[Mrbayes block for the best AICc model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17666.phylip = 1 - 211;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17666.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;


[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/chr3_17666.phylip = 1 - 211;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17666.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

