
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:10 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/chr8_6248.phylip" (19 taxa, 311 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-820.1677	1743.2226	0.2723	0.2723
HKYG	40	-825.8343	1743.8168	0.2023	0.4746
GTRI	44	-820.4924	1743.8720	0.1968	0.6714
HKYI	40	-826.1457	1744.4396	0.1482	0.8196
GTRIG	45	-819.8474	1745.3173	0.0955	0.9151
HKYIG	41	-825.4383	1745.6796	0.0797	0.9949
SYMG	41	-829.2201	1753.2431	0.0018	0.9967
SYMI	41	-829.4378	1753.6786	0.0015	0.9981
SYMIG	42	-828.9852	1755.4480	0.0006	0.9987
K2PG	37	-835.6748	1755.6500	0.0005	0.9993
K2PI	37	-836.0060	1756.3123	0.0004	0.9997
K2PIG	38	-834.8978	1756.6927	0.0003	1.0000
HKY	39	-839.8462	1769.2053	0.0000	1.0000
GTR	43	-834.5881	1769.3484	0.0000	1.0000
SYM	40	-843.7690	1779.6861	0.0000	1.0000
F81G	39	-847.3649	1784.2427	0.0000	1.0000
F81I	39	-847.6453	1784.8036	0.0000	1.0000
F81IG	40	-847.0457	1786.2395	0.0000	1.0000
K2P	36	-852.7322	1787.1871	0.0000	1.0000
JC69G	36	-853.8384	1789.3994	0.0000	1.0000
JC69I	36	-854.1002	1789.9230	0.0000	1.0000
JC69IG	37	-853.5122	1791.3247	0.0000	1.0000
F81	38	-860.8527	1808.6025	0.0000	1.0000
JC69	35	-867.5899	1814.3435	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-820.1677	1728.3354	0.3751	0.3751
GTRI	44	-820.4924	1728.9847	0.2711	0.6462
GTRIG	45	-819.8474	1729.6947	0.1901	0.8363
HKYG	40	-825.8343	1731.6687	0.0709	0.9072
HKYI	40	-826.1457	1732.2914	0.0519	0.9591
HKYIG	41	-825.4383	1732.8766	0.0387	0.9978
SYMG	41	-829.2201	1740.4401	0.0009	0.9987
SYMI	41	-829.4378	1740.8756	0.0007	0.9994
SYMIG	42	-828.9852	1741.9703	0.0004	0.9998
K2PG	37	-835.6748	1745.3497	0.0001	0.9999
K2PIG	38	-834.8978	1745.7956	0.0001	0.9999
K2PI	37	-836.0060	1746.0120	0.0001	1.0000
GTR	43	-834.5881	1755.1761	0.0000	1.0000
HKY	39	-839.8462	1757.6923	0.0000	1.0000
SYM	40	-843.7690	1767.5380	0.0000	1.0000
F81G	39	-847.3649	1772.7297	0.0000	1.0000
F81I	39	-847.6453	1773.2907	0.0000	1.0000
F81IG	40	-847.0457	1774.0913	0.0000	1.0000
K2P	36	-852.7322	1777.4645	0.0000	1.0000
JC69G	36	-853.8384	1779.6768	0.0000	1.0000
JC69I	36	-854.1002	1780.2004	0.0000	1.0000
JC69IG	37	-853.5122	1781.0243	0.0000	1.0000
F81	38	-860.8527	1797.7055	0.0000	1.0000
JC69	35	-867.5899	1805.1798	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-825.8343	1881.2604	0.4231	0.4231
HKYI	40	-826.1457	1881.8832	0.3099	0.7330
K2PG	37	-835.6748	1883.7220	0.1236	0.8566
K2PI	37	-836.0060	1884.3843	0.0887	0.9453
HKYIG	41	-825.4383	1886.2081	0.0357	0.9810
K2PIG	38	-834.8978	1887.9078	0.0152	0.9962
GTRG	44	-820.1677	1892.8862	0.0013	0.9975
GTRI	44	-820.4924	1893.5356	0.0009	0.9984
SYMG	41	-829.2201	1893.7716	0.0008	0.9992
SYMI	41	-829.4378	1894.2071	0.0007	0.9998
GTRIG	45	-819.8474	1897.9854	0.0001	0.9999
SYMIG	42	-828.9852	1899.0416	0.0001	1.0000
HKY	39	-839.8462	1903.5443	0.0000	1.0000
K2P	36	-852.7322	1912.0970	0.0000	1.0000
JC69G	36	-853.8384	1914.3094	0.0000	1.0000
JC69I	36	-854.1002	1914.8329	0.0000	1.0000
GTR	43	-834.5881	1915.9872	0.0000	1.0000
SYM	40	-843.7690	1917.1297	0.0000	1.0000
F81G	39	-847.3649	1918.5817	0.0000	1.0000
F81I	39	-847.6453	1919.1426	0.0000	1.0000
JC69IG	37	-853.5122	1919.3967	0.0000	1.0000
F81IG	40	-847.0457	1923.6831	0.0000	1.0000
JC69	35	-867.5899	1936.0726	0.0000	1.0000
F81	38	-860.8527	1939.8176	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/chr8_6248.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6248.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/chr8_6248.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6248.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6248.phylip = 1 - 311;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6248.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

