
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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/chr3_21994.phylip" (19 taxa, 340 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	-907.4630	1905.8960	0.4372	0.4372
HKYI	40	-907.6920	1906.3538	0.3477	0.7849
HKYIG	41	-907.4041	1908.3652	0.1272	0.9121
GTRG	44	-904.6141	1910.6518	0.0405	0.9527
GTRI	44	-904.7301	1910.8840	0.0361	0.9888
GTRIG	45	-904.5755	1913.2326	0.0112	0.9999
HKY	39	-917.9784	1924.3568	0.0000	1.0000
F81I	39	-920.3061	1929.0121	0.0000	1.0000
GTR	43	-915.1221	1929.0279	0.0000	1.0000
F81G	39	-920.3885	1929.1770	0.0000	1.0000
F81IG	40	-920.3883	1931.7465	0.0000	1.0000
K2PG	37	-924.2584	1931.8281	0.0000	1.0000
K2PI	37	-924.3107	1931.9326	0.0000	1.0000
K2PIG	38	-924.2541	1934.3555	0.0000	1.0000
SYMI	41	-922.1907	1937.9384	0.0000	1.0000
SYMG	41	-922.2266	1938.0102	0.0000	1.0000
SYMIG	42	-922.1292	1940.4201	0.0000	1.0000
F81	38	-930.1426	1946.1324	0.0000	1.0000
K2P	36	-934.2713	1949.3347	0.0000	1.0000
JC69I	36	-934.7859	1950.3638	0.0000	1.0000
JC69G	36	-934.8265	1950.4452	0.0000	1.0000
JC69IG	37	-934.8758	1953.0628	0.0000	1.0000
SYM	40	-932.0467	1955.0634	0.0000	1.0000
JC69	35	-944.5409	1967.3713	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-907.4630	1894.9261	0.3443	0.3443
HKYI	40	-907.6920	1895.3839	0.2738	0.6181
HKYIG	41	-907.4041	1896.8082	0.1343	0.7525
GTRG	44	-904.6141	1897.2281	0.1089	0.8614
GTRI	44	-904.7301	1897.4603	0.0970	0.9583
GTRIG	45	-904.5755	1899.1509	0.0416	1.0000
HKY	39	-917.9784	1913.9568	0.0000	1.0000
GTR	43	-915.1221	1916.2441	0.0000	1.0000
F81I	39	-920.3061	1918.6121	0.0000	1.0000
F81G	39	-920.3885	1918.7770	0.0000	1.0000
F81IG	40	-920.3883	1920.7766	0.0000	1.0000
K2PG	37	-924.2584	1922.5169	0.0000	1.0000
K2PI	37	-924.3107	1922.6213	0.0000	1.0000
K2PIG	38	-924.2541	1924.5083	0.0000	1.0000
SYMI	41	-922.1907	1926.3814	0.0000	1.0000
SYMG	41	-922.2266	1926.4532	0.0000	1.0000
SYMIG	42	-922.1292	1928.2585	0.0000	1.0000
F81	38	-930.1426	1936.2852	0.0000	1.0000
K2P	36	-934.2713	1940.5426	0.0000	1.0000
JC69I	36	-934.7859	1941.5717	0.0000	1.0000
JC69G	36	-934.8265	1941.6531	0.0000	1.0000
JC69IG	37	-934.8758	1943.7516	0.0000	1.0000
SYM	40	-932.0467	1944.0935	0.0000	1.0000
JC69	35	-944.5409	1959.0818	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-907.4630	2048.0839	0.5392	0.5392
HKYI	40	-907.6920	2048.5417	0.4289	0.9682
HKYIG	41	-907.4041	2053.7950	0.0310	0.9992
HKY	39	-917.9784	2063.2856	0.0003	0.9994
K2PG	37	-924.2584	2064.1878	0.0002	0.9996
K2PI	37	-924.3107	2064.2923	0.0002	0.9998
GTRG	44	-904.6141	2065.7017	0.0001	0.9999
GTRI	44	-904.7301	2065.9339	0.0001	0.9999
F81I	39	-920.3061	2067.9410	0.0000	1.0000
F81G	39	-920.3885	2068.1059	0.0000	1.0000
K2PIG	38	-924.2541	2070.0082	0.0000	1.0000
GTRIG	45	-904.5755	2071.4535	0.0000	1.0000
F81IG	40	-920.3883	2073.9344	0.0000	1.0000
K2P	36	-934.2713	2078.3847	0.0000	1.0000
JC69I	36	-934.7859	2079.4138	0.0000	1.0000
JC69G	36	-934.8265	2079.4951	0.0000	1.0000
GTR	43	-915.1221	2080.8888	0.0000	1.0000
F81	38	-930.1426	2081.7851	0.0000	1.0000
SYMI	41	-922.1907	2083.3681	0.0000	1.0000
SYMG	41	-922.2266	2083.4400	0.0000	1.0000
JC69IG	37	-934.8758	2085.4225	0.0000	1.0000
SYMIG	42	-922.1292	2089.0742	0.0000	1.0000
JC69	35	-944.5409	2093.0949	0.0000	1.0000
SYM	40	-932.0467	2097.2513	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/chr3_21994.phylip = 1 - 340;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21994.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/chr3_21994.phylip = 1 - 340;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21994.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/chr3_21994.phylip = 1 - 340;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21994.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;


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

