
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:17 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/chr11_6387.phylip" (19 taxa, 256 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-745.7926	1598.3531	0.3268	0.3268
HKYG	40	-751.9705	1599.1968	0.2143	0.5412
HKYI	40	-752.5544	1600.3646	0.1195	0.6607
GTRIG	45	-745.7515	1601.2174	0.0780	0.7387
SYMG	41	-751.7167	1601.5269	0.0669	0.8056
HKYIG	41	-751.8986	1601.8906	0.0557	0.8613
GTRI	44	-747.5847	1601.9372	0.0545	0.9158
SYMI	41	-752.2823	1602.6581	0.0380	0.9538
SYMIG	42	-751.7105	1604.3786	0.0161	0.9698
K2PG	37	-758.7659	1604.4308	0.0157	0.9855
K2PI	37	-759.1669	1605.2329	0.0105	0.9960
K2PIG	38	-758.7409	1607.1407	0.0040	1.0000
GTR	43	-761.2188	1626.2866	0.0000	1.0000
HKY	39	-771.5506	1635.5456	0.0000	1.0000
SYM	40	-771.0918	1637.4395	0.0000	1.0000
K2P	36	-778.7500	1641.6644	0.0000	1.0000
F81G	39	-776.1483	1644.7410	0.0000	1.0000
F81I	39	-776.2720	1644.9885	0.0000	1.0000
F81IG	40	-776.1523	1647.5605	0.0000	1.0000
JC69G	36	-784.6260	1653.4163	0.0000	1.0000
JC69I	36	-784.6987	1653.5618	0.0000	1.0000
JC69IG	37	-784.6257	1656.1505	0.0000	1.0000
F81	38	-793.1966	1676.0521	0.0000	1.0000
JC69	35	-800.9949	1683.4444	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-745.7926	1579.5853	0.5318	0.5318
GTRIG	45	-745.7515	1581.5031	0.2038	0.7356
GTRI	44	-747.5847	1583.1694	0.0886	0.8242
HKYG	40	-751.9705	1583.9410	0.0602	0.8845
HKYI	40	-752.5544	1585.1088	0.0336	0.9181
SYMG	41	-751.7167	1585.4334	0.0286	0.9466
HKYIG	41	-751.8986	1585.7971	0.0238	0.9704
SYMI	41	-752.2823	1586.5646	0.0162	0.9867
SYMIG	42	-751.7105	1587.4209	0.0106	0.9972
K2PG	37	-758.7659	1591.5317	0.0014	0.9986
K2PI	37	-759.1669	1592.3338	0.0009	0.9995
K2PIG	38	-758.7409	1593.4817	0.0005	1.0000
GTR	43	-761.2188	1608.4376	0.0000	1.0000
HKY	39	-771.5506	1621.1011	0.0000	1.0000
SYM	40	-771.0918	1622.1837	0.0000	1.0000
K2P	36	-778.7500	1629.5000	0.0000	1.0000
F81G	39	-776.1483	1630.2965	0.0000	1.0000
F81I	39	-776.2720	1630.5441	0.0000	1.0000
F81IG	40	-776.1523	1632.3047	0.0000	1.0000
JC69G	36	-784.6260	1641.2520	0.0000	1.0000
JC69I	36	-784.6987	1641.3974	0.0000	1.0000
JC69IG	37	-784.6257	1643.2514	0.0000	1.0000
F81	38	-793.1966	1662.3931	0.0000	1.0000
JC69	35	-800.9949	1671.9899	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-758.7659	1722.7033	0.4719	0.4719
K2PI	37	-759.1669	1723.5054	0.3160	0.7880
HKYG	40	-751.9705	1725.7481	0.1030	0.8909
HKYI	40	-752.5544	1726.9159	0.0574	0.9484
K2PIG	38	-758.7409	1728.1985	0.0302	0.9786
SYMG	41	-751.7167	1730.7857	0.0083	0.9869
HKYIG	41	-751.8986	1731.1494	0.0069	0.9938
SYMI	41	-752.2823	1731.9169	0.0047	0.9985
GTRG	44	-745.7926	1735.5731	0.0008	0.9993
SYMIG	42	-751.7105	1736.3184	0.0005	0.9998
GTRI	44	-747.5847	1739.1572	0.0001	1.0000
GTRIG	45	-745.7515	1741.0361	0.0000	1.0000
K2P	36	-778.7500	1757.1264	0.0000	1.0000
HKY	39	-771.5506	1759.3630	0.0000	1.0000
GTR	43	-761.2188	1760.8802	0.0000	1.0000
SYM	40	-771.0918	1763.9908	0.0000	1.0000
F81G	39	-776.1483	1768.5584	0.0000	1.0000
F81I	39	-776.2720	1768.8060	0.0000	1.0000
JC69G	36	-784.6260	1768.8783	0.0000	1.0000
JC69I	36	-784.6987	1769.0238	0.0000	1.0000
F81IG	40	-776.1523	1774.1118	0.0000	1.0000
JC69IG	37	-784.6257	1774.4230	0.0000	1.0000
JC69	35	-800.9949	1796.0711	0.0000	1.0000
F81	38	-793.1966	1797.1099	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/chr11_6387.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6387.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6387.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6387.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 BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6387.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6387.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

