
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:04 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_11467.phylip" (19 taxa, 289 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	-739.4555	1572.1369	0.4288	0.4288
HKYI	40	-739.6334	1572.4926	0.3589	0.7878
HKYIG	41	-739.1105	1574.1643	0.1556	0.9434
GTRG	44	-736.7134	1577.6564	0.0271	0.9705
GTRI	44	-737.1850	1578.5995	0.0169	0.9875
GTRIG	45	-736.0822	1579.2015	0.0125	1.0000
HKY	39	-754.4124	1599.3549	0.0000	1.0000
GTR	43	-751.1717	1603.7883	0.0000	1.0000
F81G	39	-758.2833	1607.0967	0.0000	1.0000
F81I	39	-758.5386	1607.6073	0.0000	1.0000
F81IG	40	-757.8469	1608.9197	0.0000	1.0000
K2PG	37	-763.1839	1611.5710	0.0000	1.0000
K2PI	37	-763.4368	1612.0767	0.0000	1.0000
K2PIG	38	-762.4186	1612.6932	0.0000	1.0000
SYMG	41	-761.9852	1619.9137	0.0000	1.0000
SYMI	41	-762.2185	1620.3804	0.0000	1.0000
SYMIG	42	-761.1941	1621.0711	0.0000	1.0000
F81	38	-772.4607	1632.7774	0.0000	1.0000
K2P	36	-778.2099	1638.9911	0.0000	1.0000
JC69G	36	-778.3618	1639.2951	0.0000	1.0000
JC69I	36	-778.5943	1639.7600	0.0000	1.0000
JC69IG	37	-777.8601	1640.9234	0.0000	1.0000
SYM	40	-777.0611	1647.3480	0.0000	1.0000
JC69	35	-792.8642	1665.6888	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-739.4555	1558.9111	0.3317	0.3317
HKYI	40	-739.6334	1559.2668	0.2777	0.6094
HKYIG	41	-739.1105	1560.2210	0.1723	0.7817
GTRG	44	-736.7134	1561.4269	0.0943	0.8760
GTRIG	45	-736.0822	1562.1644	0.0652	0.9412
GTRI	44	-737.1850	1562.3700	0.0588	1.0000
HKY	39	-754.4124	1586.8248	0.0000	1.0000
GTR	43	-751.1717	1588.3434	0.0000	1.0000
F81G	39	-758.2833	1594.5666	0.0000	1.0000
F81I	39	-758.5386	1595.0772	0.0000	1.0000
F81IG	40	-757.8469	1595.6939	0.0000	1.0000
K2PG	37	-763.1839	1600.3678	0.0000	1.0000
K2PIG	38	-762.4186	1600.8372	0.0000	1.0000
K2PI	37	-763.4368	1600.8736	0.0000	1.0000
SYMG	41	-761.9852	1605.9704	0.0000	1.0000
SYMIG	42	-761.1941	1606.3882	0.0000	1.0000
SYMI	41	-762.2185	1606.4371	0.0000	1.0000
F81	38	-772.4607	1620.9214	0.0000	1.0000
K2P	36	-778.2099	1628.4197	0.0000	1.0000
JC69G	36	-778.3618	1628.7237	0.0000	1.0000
JC69I	36	-778.5943	1629.1886	0.0000	1.0000
JC69IG	37	-777.8601	1629.7202	0.0000	1.0000
SYM	40	-777.0611	1634.1222	0.0000	1.0000
JC69	35	-792.8642	1655.7284	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-739.4555	1705.5681	0.5207	0.5207
HKYI	40	-739.6334	1705.9239	0.4359	0.9566
HKYIG	41	-739.1105	1710.5445	0.0433	0.9998
GTRG	44	-736.7134	1722.7497	0.0001	0.9999
GTRI	44	-737.1850	1723.6928	0.0001	1.0000
GTRIG	45	-736.0822	1727.1536	0.0000	1.0000
HKY	39	-754.4124	1729.8154	0.0000	1.0000
K2PG	37	-763.1839	1736.0256	0.0000	1.0000
K2PI	37	-763.4368	1736.5313	0.0000	1.0000
F81G	39	-758.2833	1737.5572	0.0000	1.0000
F81I	39	-758.5386	1738.0678	0.0000	1.0000
K2PIG	38	-762.4186	1740.1615	0.0000	1.0000
F81IG	40	-757.8469	1742.3509	0.0000	1.0000
GTR	43	-751.1717	1745.9997	0.0000	1.0000
SYMG	41	-761.9852	1756.2939	0.0000	1.0000
SYMI	41	-762.2185	1756.7606	0.0000	1.0000
F81	38	-772.4607	1760.2457	0.0000	1.0000
SYMIG	42	-761.1941	1760.3781	0.0000	1.0000
K2P	36	-778.2099	1760.4111	0.0000	1.0000
JC69G	36	-778.3618	1760.7150	0.0000	1.0000
JC69I	36	-778.5943	1761.1800	0.0000	1.0000
JC69IG	37	-777.8601	1765.3780	0.0000	1.0000
SYM	40	-777.0611	1780.7793	0.0000	1.0000
JC69	35	-792.8642	1784.0533	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_11467.phylip = 1 - 289;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11467.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_11467.phylip = 1 - 289;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11467.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_11467.phylip = 1 - 289;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11467.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

