
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:07 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_3451.phylip" (19 taxa, 617 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	-1863.2330	3821.3890	0.5030	0.5030
GTRI	44	-1863.7250	3822.3731	0.3075	0.8105
GTRIG	45	-1863.1289	3823.5082	0.1743	0.9848
HKYG	40	-1872.1393	3829.9730	0.0069	0.9917
HKYI	40	-1872.2956	3830.2855	0.0059	0.9975
HKYIG	41	-1872.0189	3832.0273	0.0025	1.0000
GTR	43	-1886.1457	3864.8953	0.0000	1.0000
HKY	39	-1893.2308	3869.8690	0.0000	1.0000
K2PG	37	-1906.8434	3892.5434	0.0000	1.0000
K2PI	37	-1906.8595	3892.5757	0.0000	1.0000
SYMG	41	-1902.7209	3893.4314	0.0000	1.0000
SYMI	41	-1902.7493	3893.4881	0.0000	1.0000
K2PIG	38	-1906.6854	3894.4989	0.0000	1.0000
SYMIG	42	-1902.5669	3895.4264	0.0000	1.0000
F81I	39	-1912.0195	3907.4463	0.0000	1.0000
F81G	39	-1912.1029	3907.6131	0.0000	1.0000
F81IG	40	-1911.9188	3909.5320	0.0000	1.0000
K2P	36	-1927.2254	3931.0438	0.0000	1.0000
SYM	40	-1923.6076	3932.9097	0.0000	1.0000
F81	38	-1931.6385	3944.4050	0.0000	1.0000
JC69I	36	-1940.1853	3956.9636	0.0000	1.0000
JC69G	36	-1940.2883	3957.1696	0.0000	1.0000
JC69IG	37	-1940.2933	3959.4432	0.0000	1.0000
JC69	35	-1959.7068	3993.7509	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1863.2330	3814.4659	0.4911	0.4911
GTRI	44	-1863.7250	3815.4500	0.3002	0.7913
GTRIG	45	-1863.1289	3816.2578	0.2005	0.9918
HKYG	40	-1872.1393	3824.2786	0.0036	0.9954
HKYI	40	-1872.2956	3824.5911	0.0031	0.9985
HKYIG	41	-1872.0189	3826.0378	0.0015	1.0000
GTR	43	-1886.1457	3858.2914	0.0000	1.0000
HKY	39	-1893.2308	3864.4617	0.0000	1.0000
SYMG	41	-1902.7209	3887.4419	0.0000	1.0000
SYMI	41	-1902.7493	3887.4985	0.0000	1.0000
K2PG	37	-1906.8434	3887.6868	0.0000	1.0000
K2PI	37	-1906.8595	3887.7190	0.0000	1.0000
SYMIG	42	-1902.5669	3889.1337	0.0000	1.0000
K2PIG	38	-1906.6854	3889.3709	0.0000	1.0000
F81I	39	-1912.0195	3902.0390	0.0000	1.0000
F81G	39	-1912.1029	3902.2059	0.0000	1.0000
F81IG	40	-1911.9188	3903.8376	0.0000	1.0000
K2P	36	-1927.2254	3926.4507	0.0000	1.0000
SYM	40	-1923.6076	3927.2152	0.0000	1.0000
F81	38	-1931.6385	3939.2769	0.0000	1.0000
JC69I	36	-1940.1853	3952.3705	0.0000	1.0000
JC69G	36	-1940.2883	3952.5765	0.0000	1.0000
JC69IG	37	-1940.2933	3954.5865	0.0000	1.0000
JC69	35	-1959.7068	3989.4136	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1872.1393	4001.2734	0.5174	0.5174
HKYI	40	-1872.2956	4001.5859	0.4425	0.9599
HKYIG	41	-1872.0189	4007.4574	0.0235	0.9834
GTRG	44	-1863.2330	4009.1602	0.0100	0.9934
GTRI	44	-1863.7250	4010.1442	0.0061	0.9996
GTRIG	45	-1863.1289	4015.3769	0.0004	1.0000
HKY	39	-1893.2308	4037.0316	0.0000	1.0000
GTR	43	-1886.1457	4048.5608	0.0000	1.0000
K2PG	37	-1906.8434	4051.4070	0.0000	1.0000
K2PI	37	-1906.8595	4051.4392	0.0000	1.0000
K2PIG	38	-1906.6854	4057.5159	0.0000	1.0000
SYMG	41	-1902.7209	4068.8615	0.0000	1.0000
SYMI	41	-1902.7493	4068.9181	0.0000	1.0000
F81I	39	-1912.0195	4074.6089	0.0000	1.0000
F81G	39	-1912.1029	4074.7758	0.0000	1.0000
SYMIG	42	-1902.5669	4074.9782	0.0000	1.0000
F81IG	40	-1911.9188	4080.8323	0.0000	1.0000
K2P	36	-1927.2254	4085.7460	0.0000	1.0000
SYM	40	-1923.6076	4104.2100	0.0000	1.0000
F81	38	-1931.6385	4107.4220	0.0000	1.0000
JC69I	36	-1940.1853	4111.6658	0.0000	1.0000
JC69G	36	-1940.2883	4111.8718	0.0000	1.0000
JC69IG	37	-1940.2933	4118.3067	0.0000	1.0000
JC69	35	-1959.7068	4144.2840	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_3451.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3451.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_3451.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3451.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_3451.phylip = 1 - 617;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3451.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

