
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:35 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/chr1_7683.phylip" (19 taxa, 234 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-894.7887	1886.5722	0.4714	0.4714
HKYI	40	-894.9386	1886.8721	0.4057	0.8771
HKYIG	41	-894.7692	1889.4760	0.1104	0.9875
GTRG	44	-893.1830	1895.3183	0.0059	0.9934
GTRI	44	-893.3298	1895.6120	0.0051	0.9986
GTRIG	45	-893.1506	1898.3225	0.0013	0.9999
HKY	39	-904.6509	1903.3843	0.0001	1.0000
K2PG	37	-910.9651	1910.2771	0.0000	1.0000
K2PI	37	-911.3423	1911.0315	0.0000	1.0000
GTR	43	-903.5204	1912.9565	0.0000	1.0000
K2PIG	38	-910.9682	1913.1364	0.0000	1.0000
SYMG	41	-910.5005	1920.9385	0.0000	1.0000
SYMI	41	-910.9280	1921.7936	0.0000	1.0000
SYMIG	42	-910.5004	1923.9118	0.0000	1.0000
F81G	39	-915.3835	1924.8495	0.0000	1.0000
F81I	39	-915.4671	1925.0167	0.0000	1.0000
K2P	36	-920.4894	1926.5017	0.0000	1.0000
F81IG	40	-915.3763	1927.7473	0.0000	1.0000
SYM	40	-920.1093	1937.2135	0.0000	1.0000
F81	38	-924.2145	1939.6289	0.0000	1.0000
JC69G	36	-927.5986	1940.7200	0.0000	1.0000
JC69I	36	-927.8173	1941.1574	0.0000	1.0000
JC69IG	37	-927.6090	1943.5650	0.0000	1.0000
JC69	35	-936.4685	1955.6643	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-894.7887	1869.5774	0.4097	0.4097
HKYI	40	-894.9386	1869.8773	0.3527	0.7624
HKYIG	41	-894.7692	1871.5385	0.1537	0.9161
GTRG	44	-893.1830	1874.3659	0.0374	0.9535
GTRI	44	-893.3298	1874.6596	0.0323	0.9857
GTRIG	45	-893.1506	1876.3012	0.0142	0.9999
HKY	39	-904.6509	1887.3019	0.0001	1.0000
GTR	43	-903.5204	1893.0408	0.0000	1.0000
K2PG	37	-910.9651	1895.9301	0.0000	1.0000
K2PI	37	-911.3423	1896.6846	0.0000	1.0000
K2PIG	38	-910.9682	1897.9364	0.0000	1.0000
SYMG	41	-910.5005	1903.0010	0.0000	1.0000
SYMI	41	-910.9280	1903.8561	0.0000	1.0000
SYMIG	42	-910.5004	1905.0008	0.0000	1.0000
F81G	39	-915.3835	1908.7670	0.0000	1.0000
F81I	39	-915.4671	1908.9342	0.0000	1.0000
F81IG	40	-915.3763	1910.7525	0.0000	1.0000
K2P	36	-920.4894	1912.9789	0.0000	1.0000
SYM	40	-920.1093	1920.2187	0.0000	1.0000
F81	38	-924.2145	1924.4289	0.0000	1.0000
JC69G	36	-927.5986	1927.1972	0.0000	1.0000
JC69I	36	-927.8173	1927.6345	0.0000	1.0000
JC69IG	37	-927.6090	1929.2180	0.0000	1.0000
JC69	35	-936.4685	1942.9370	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-894.7887	2007.7902	0.5184	0.5184
HKYI	40	-894.9386	2008.0901	0.4462	0.9646
HKYIG	41	-894.7692	2013.2066	0.0346	0.9992
HKY	39	-904.6509	2022.0594	0.0004	0.9996
K2PG	37	-910.9651	2023.7770	0.0002	0.9998
K2PI	37	-911.3423	2024.5315	0.0001	0.9999
GTRG	44	-893.1830	2026.4000	0.0000	0.9999
GTRI	44	-893.3298	2026.6937	0.0000	1.0000
K2PIG	38	-910.9682	2029.2386	0.0000	1.0000
GTRIG	45	-893.1506	2031.7907	0.0000	1.0000
K2P	36	-920.4894	2037.3704	0.0000	1.0000
GTR	43	-903.5204	2041.6196	0.0000	1.0000
F81G	39	-915.3835	2043.5245	0.0000	1.0000
F81I	39	-915.4671	2043.6917	0.0000	1.0000
SYMG	41	-910.5005	2044.6691	0.0000	1.0000
SYMI	41	-910.9280	2045.5242	0.0000	1.0000
F81IG	40	-915.3763	2048.9654	0.0000	1.0000
SYMIG	42	-910.5004	2050.1243	0.0000	1.0000
JC69G	36	-927.5986	2051.5887	0.0000	1.0000
JC69I	36	-927.8173	2052.0261	0.0000	1.0000
F81	38	-924.2145	2055.7311	0.0000	1.0000
JC69IG	37	-927.6090	2057.0649	0.0000	1.0000
SYM	40	-920.1093	2058.4315	0.0000	1.0000
JC69	35	-936.4685	2063.8732	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7683.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7683.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7683.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7683.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;


[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/chr1_7683.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7683.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

