
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:13 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/chr4_10540.phylip" (19 taxa, 319 characters)

Minimum AIC  model: K2PG
Minimum AICc model: K2PG
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
K2PG	37	-914.9194	1913.8459	0.4874	0.4874
K2PI	37	-915.4385	1914.8841	0.2901	0.7775
K2PIG	38	-914.8028	1916.1913	0.1509	0.9284
HKYG	40	-914.0839	1919.9663	0.0229	0.9512
SYMG	41	-913.2256	1920.8843	0.0144	0.9657
HKYI	40	-914.6611	1921.1207	0.0128	0.9785
SYMI	41	-913.6848	1921.8029	0.0091	0.9876
HKYIG	41	-913.9528	1922.3387	0.0070	0.9946
SYMIG	42	-913.1570	1923.4010	0.0041	0.9987
GTRG	44	-912.2590	1926.9705	0.0007	0.9994
GTRI	44	-912.7871	1928.0267	0.0004	0.9998
GTRIG	45	-912.1795	1929.5238	0.0002	1.0000
K2P	36	-926.7027	1934.8522	0.0000	1.0000
HKY	39	-925.5382	1940.2591	0.0000	1.0000
SYM	40	-924.3499	1940.4984	0.0000	1.0000
GTR	43	-922.8885	1945.5370	0.0000	1.0000
JC69G	36	-940.1231	1961.6929	0.0000	1.0000
JC69I	36	-940.6108	1962.6685	0.0000	1.0000
JC69IG	37	-940.0484	1964.1040	0.0000	1.0000
F81G	39	-939.2516	1967.6859	0.0000	1.0000
F81I	39	-939.7659	1968.7146	0.0000	1.0000
F81IG	40	-939.1707	1970.1400	0.0000	1.0000
JC69	35	-951.5279	1981.9603	0.0000	1.0000
F81	38	-950.4866	1987.5590	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
K2PG	37	-914.9194	1903.8388	0.4059	0.4059
K2PI	37	-915.4385	1904.8770	0.2415	0.6474
K2PIG	38	-914.8028	1905.6056	0.1678	0.8152
HKYG	40	-914.0839	1908.1678	0.0466	0.8618
SYMG	41	-913.2256	1908.4511	0.0404	0.9023
HKYI	40	-914.6611	1909.3222	0.0262	0.9284
SYMI	41	-913.6848	1909.3697	0.0256	0.9540
HKYIG	41	-913.9528	1909.9055	0.0195	0.9735
SYMIG	42	-913.1570	1910.3141	0.0159	0.9895
GTRG	44	-912.2590	1912.5179	0.0053	0.9948
GTRI	44	-912.7871	1913.5741	0.0031	0.9979
GTRIG	45	-912.1795	1914.3590	0.0021	1.0000
K2P	36	-926.7027	1925.4054	0.0000	1.0000
SYM	40	-924.3499	1928.6998	0.0000	1.0000
HKY	39	-925.5382	1929.0763	0.0000	1.0000
GTR	43	-922.8885	1931.7770	0.0000	1.0000
JC69G	36	-940.1231	1952.2461	0.0000	1.0000
JC69I	36	-940.6108	1953.2217	0.0000	1.0000
JC69IG	37	-940.0484	1954.0968	0.0000	1.0000
F81G	39	-939.2516	1956.5031	0.0000	1.0000
F81I	39	-939.7659	1957.5318	0.0000	1.0000
F81IG	40	-939.1707	1958.3415	0.0000	1.0000
JC69	35	-951.5279	1973.0557	0.0000	1.0000
F81	38	-950.4866	1976.9732	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-914.9194	2043.1508	0.6028	0.6028
K2PI	37	-915.4385	2044.1891	0.3587	0.9615
K2PIG	38	-914.8028	2048.6828	0.0379	0.9995
HKYG	40	-914.0839	2058.7754	0.0002	0.9997
HKYI	40	-914.6611	2059.9298	0.0001	0.9998
K2P	36	-926.7027	2060.9523	0.0001	0.9999
SYMG	41	-913.2256	2062.8240	0.0000	1.0000
SYMI	41	-913.6848	2063.7425	0.0000	1.0000
HKYIG	41	-913.9528	2064.2783	0.0000	1.0000
SYMIG	42	-913.1570	2068.4521	0.0000	1.0000
HKY	39	-925.5382	2075.9188	0.0000	1.0000
GTRG	44	-912.2590	2078.1863	0.0000	1.0000
GTRI	44	-912.7871	2079.2425	0.0000	1.0000
SYM	40	-924.3499	2079.3075	0.0000	1.0000
GTRIG	45	-912.1795	2083.7926	0.0000	1.0000
JC69G	36	-940.1231	2087.7930	0.0000	1.0000
JC69I	36	-940.6108	2088.7686	0.0000	1.0000
JC69IG	37	-940.0484	2093.4089	0.0000	1.0000
GTR	43	-922.8885	2093.6802	0.0000	1.0000
F81G	39	-939.2516	2103.3456	0.0000	1.0000
F81I	39	-939.7659	2104.3743	0.0000	1.0000
JC69	35	-951.5279	2104.8374	0.0000	1.0000
F81IG	40	-939.1707	2108.9491	0.0000	1.0000
F81	38	-950.4866	2120.0505	0.0000	1.0000



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

[Mrbayes block for the best AIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10540.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10540.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;


[Mrbayes block for the best AICc model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10540.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10540.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;


[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/chr4_10540.phylip = 1 - 319;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10540.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

