
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:19 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/chr15_3483.phylip" (19 taxa, 272 characters)

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


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	-842.1742	1781.3223	0.8287	0.8287
GTRIG	45	-838.3550	1785.0286	0.1299	0.9586
GTRG	44	-841.6048	1788.6545	0.0212	0.9798
HKYI	40	-847.8641	1789.9274	0.0112	0.9910
HKYG	40	-848.3966	1790.9923	0.0066	0.9976
GTRI	44	-843.8052	1793.0554	0.0023	1.0000
K2PIG	38	-856.7215	1802.1640	0.0000	1.0000
SYMIG	42	-852.4795	1804.7319	0.0000	1.0000
K2PI	37	-862.0827	1810.1825	0.0000	1.0000
K2PG	37	-862.5834	1811.1839	0.0000	1.0000
SYMI	41	-858.3612	1813.6962	0.0000	1.0000
SYMG	41	-859.0254	1815.0246	0.0000	1.0000
F81IG	40	-865.2070	1824.6130	0.0000	1.0000
F81G	39	-869.6740	1830.7963	0.0000	1.0000
F81I	39	-870.6103	1832.6689	0.0000	1.0000
JC69IG	37	-880.4379	1846.8928	0.0000	1.0000
JC69G	36	-883.3548	1850.0457	0.0000	1.0000
JC69I	36	-884.6612	1852.6585	0.0000	1.0000
GTR	43	-904.8368	1912.2701	0.0000	1.0000
HKY	39	-910.6295	1912.7073	0.0000	1.0000
K2P	36	-922.6256	1928.5874	0.0000	1.0000
SYM	40	-920.4044	1935.0079	0.0000	1.0000
F81	38	-927.9040	1944.5290	0.0000	1.0000
JC69	35	-943.4034	1967.4847	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-842.1742	1766.3484	0.5136	0.5136
GTRIG	45	-838.3550	1766.7100	0.4287	0.9423
GTRG	44	-841.6048	1771.2096	0.0452	0.9875
GTRI	44	-843.8052	1775.6104	0.0050	0.9925
HKYI	40	-847.8641	1775.7283	0.0047	0.9972
HKYG	40	-848.3966	1776.7931	0.0028	1.0000
SYMIG	42	-852.4795	1788.9590	0.0000	1.0000
K2PIG	38	-856.7215	1789.4430	0.0000	1.0000
K2PI	37	-862.0827	1798.1654	0.0000	1.0000
SYMI	41	-858.3612	1798.7223	0.0000	1.0000
K2PG	37	-862.5834	1799.1668	0.0000	1.0000
SYMG	41	-859.0254	1800.0507	0.0000	1.0000
F81IG	40	-865.2070	1810.4139	0.0000	1.0000
F81G	39	-869.6740	1817.3480	0.0000	1.0000
F81I	39	-870.6103	1819.2206	0.0000	1.0000
JC69IG	37	-880.4379	1834.8757	0.0000	1.0000
JC69G	36	-883.3548	1838.7096	0.0000	1.0000
JC69I	36	-884.6612	1841.3223	0.0000	1.0000
GTR	43	-904.8368	1895.6736	0.0000	1.0000
HKY	39	-910.6295	1899.2590	0.0000	1.0000
K2P	36	-922.6256	1917.2512	0.0000	1.0000
SYM	40	-920.4044	1920.8087	0.0000	1.0000
F81	38	-927.9040	1931.8079	0.0000	1.0000
JC69	35	-943.4034	1956.8067	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-842.1742	1914.1863	0.9158	0.9158
HKYI	40	-847.8641	1919.9604	0.0510	0.9668
HKYG	40	-848.3966	1921.0252	0.0300	0.9968
K2PIG	38	-856.7215	1926.4635	0.0020	0.9988
GTRIG	45	-838.3550	1928.9711	0.0006	0.9994
GTRG	44	-841.6048	1929.8649	0.0004	0.9997
K2PI	37	-862.0827	1931.5800	0.0002	0.9999
K2PG	37	-862.5834	1932.5815	0.0001	1.0000
GTRI	44	-843.8052	1934.2657	0.0000	1.0000
SYMIG	42	-852.4795	1940.4027	0.0000	1.0000
SYMI	41	-858.3612	1946.5602	0.0000	1.0000
SYMG	41	-859.0254	1947.8886	0.0000	1.0000
F81IG	40	-865.2070	1954.6460	0.0000	1.0000
F81G	39	-869.6740	1957.9743	0.0000	1.0000
F81I	39	-870.6103	1959.8469	0.0000	1.0000
JC69IG	37	-880.4379	1968.2904	0.0000	1.0000
JC69G	36	-883.3548	1968.5184	0.0000	1.0000
JC69I	36	-884.6612	1971.1312	0.0000	1.0000
HKY	39	-910.6295	2039.8853	0.0000	1.0000
K2P	36	-922.6256	2047.0601	0.0000	1.0000
GTR	43	-904.8368	2050.7230	0.0000	1.0000
SYM	40	-920.4044	2065.0408	0.0000	1.0000
F81	38	-927.9040	2068.8284	0.0000	1.0000
JC69	35	-943.4034	2083.0098	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/chr15_3483.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr15_3483.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/chr15_3483.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr15_3483.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr15_3483.phylip = 1 - 272;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr15_3483.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;


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End of Output

