
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:02 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/chr9_6320.phylip" (19 taxa, 259 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: K2PIG


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
HKYIG	41	-802.0790	1702.0289	0.6266	0.6266
K2PIG	38	-807.8487	1705.1702	0.1303	0.7568
HKYG	40	-805.4554	1705.9566	0.0879	0.8447
HKYI	40	-805.6251	1706.2962	0.0742	0.9189
GTRIG	45	-799.0774	1707.5915	0.0388	0.9578
K2PG	37	-811.4404	1709.6047	0.0142	0.9719
K2PI	37	-811.6041	1709.9321	0.0120	0.9840
GTRG	44	-802.1057	1710.7162	0.0081	0.9921
GTRI	44	-802.3781	1711.2609	0.0062	0.9983
SYMIG	42	-806.8135	1714.3492	0.0013	0.9997
SYMG	41	-810.1810	1718.2330	0.0002	0.9998
SYMI	41	-810.3661	1718.6032	0.0002	1.0000
F81G	39	-832.4059	1757.0584	0.0000	1.0000
F81IG	40	-832.8067	1760.6592	0.0000	1.0000
F81I	39	-835.4345	1763.1156	0.0000	1.0000
JC69IG	37	-839.7708	1766.2656	0.0000	1.0000
JC69G	36	-842.1464	1768.2929	0.0000	1.0000
JC69I	36	-842.2504	1768.5009	0.0000	1.0000
HKY	39	-846.6272	1785.5009	0.0000	1.0000
K2P	36	-852.6116	1789.2232	0.0000	1.0000
GTR	43	-843.4997	1790.5994	0.0000	1.0000
SYM	40	-849.0679	1793.1817	0.0000	1.0000
F81	38	-867.9546	1825.3818	0.0000	1.0000
JC69	35	-876.0522	1833.4049	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-802.0790	1686.1580	0.5881	0.5881
GTRIG	45	-799.0774	1688.1548	0.2167	0.8049
HKYG	40	-805.4554	1690.9108	0.0546	0.8595
HKYI	40	-805.6251	1691.2503	0.0461	0.9056
K2PIG	38	-807.8487	1691.6975	0.0369	0.9424
GTRG	44	-802.1057	1692.2115	0.0285	0.9710
GTRI	44	-802.3781	1692.7562	0.0217	0.9927
K2PG	37	-811.4404	1696.8807	0.0028	0.9954
K2PI	37	-811.6041	1697.2082	0.0023	0.9978
SYMIG	42	-806.8135	1697.6270	0.0019	0.9997
SYMG	41	-810.1810	1702.3621	0.0002	0.9999
SYMI	41	-810.3661	1702.7322	0.0001	1.0000
F81G	39	-832.4059	1742.8118	0.0000	1.0000
F81IG	40	-832.8067	1745.6133	0.0000	1.0000
F81I	39	-835.4345	1748.8691	0.0000	1.0000
JC69IG	37	-839.7708	1753.5416	0.0000	1.0000
JC69G	36	-842.1464	1756.2929	0.0000	1.0000
JC69I	36	-842.2504	1756.5009	0.0000	1.0000
HKY	39	-846.6272	1771.2544	0.0000	1.0000
GTR	43	-843.4997	1772.9994	0.0000	1.0000
K2P	36	-852.6116	1777.2232	0.0000	1.0000
SYM	40	-849.0679	1778.1358	0.0000	1.0000
F81	38	-867.9546	1811.9091	0.0000	1.0000
JC69	35	-876.0522	1822.1044	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PIG	38	-807.8487	1826.8570	0.5064	0.5064
K2PG	37	-811.4404	1828.4834	0.2245	0.7309
K2PI	37	-811.6041	1828.8108	0.1906	0.9215
HKYIG	41	-802.0790	1831.9879	0.0389	0.9605
HKYG	40	-805.4554	1833.1839	0.0214	0.9819
HKYI	40	-805.6251	1833.5234	0.0181	0.9999
SYMIG	42	-806.8135	1847.0138	0.0000	1.0000
SYMG	41	-810.1810	1848.1920	0.0000	1.0000
GTRIG	45	-799.0774	1848.2121	0.0000	1.0000
SYMI	41	-810.3661	1848.5622	0.0000	1.0000
GTRG	44	-802.1057	1848.7119	0.0000	1.0000
GTRI	44	-802.3781	1849.2567	0.0000	1.0000
F81G	39	-832.4059	1881.5281	0.0000	1.0000
JC69G	36	-842.1464	1884.3387	0.0000	1.0000
JC69I	36	-842.2504	1884.5467	0.0000	1.0000
JC69IG	37	-839.7708	1885.1442	0.0000	1.0000
F81I	39	-835.4345	1887.5854	0.0000	1.0000
F81IG	40	-832.8067	1887.8865	0.0000	1.0000
K2P	36	-852.6116	1905.2690	0.0000	1.0000
HKY	39	-846.6272	1909.9707	0.0000	1.0000
SYM	40	-849.0679	1920.4089	0.0000	1.0000
GTR	43	-843.4997	1925.9430	0.0000	1.0000
JC69	35	-876.0522	1946.5934	0.0000	1.0000
F81	38	-867.9546	1947.0686	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip = 1 - 259;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6320.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


-------------------------------------------------------------
End of Output

