
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:39 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/chr6_9625.phylip" (19 taxa, 508 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-1868.3758	3833.3045	0.6868	0.6868
GTRIG	45	-1867.9586	3834.8781	0.3127	0.9994
GTRI	44	-1875.4437	3847.4404	0.0006	1.0000
HKYG	40	-1896.1274	3879.2783	0.0000	1.0000
HKYIG	41	-1895.7589	3880.9083	0.0000	1.0000
SYMG	41	-1895.7798	3880.9502	0.0000	1.0000
SYMIG	42	-1895.2978	3882.3634	0.0000	1.0000
HKYI	40	-1899.6813	3886.3861	0.0000	1.0000
SYMI	41	-1899.9602	3889.3109	0.0000	1.0000
K2PG	37	-1909.1991	3898.3812	0.0000	1.0000
K2PIG	38	-1908.8591	3900.0381	0.0000	1.0000
K2PI	37	-1912.6725	3905.3280	0.0000	1.0000
GTR	43	-1921.4634	3937.0820	0.0000	1.0000
HKY	39	-1942.9657	3970.5980	0.0000	1.0000
F81G	39	-1944.2456	3973.1578	0.0000	1.0000
SYM	40	-1943.1563	3973.3361	0.0000	1.0000
F81IG	40	-1944.0362	3975.0959	0.0000	1.0000
F81I	39	-1947.0825	3978.8316	0.0000	1.0000
K2P	36	-1955.3855	3988.4271	0.0000	1.0000
JC69G	36	-1958.2226	3994.1012	0.0000	1.0000
JC69IG	37	-1958.0955	3996.1740	0.0000	1.0000
JC69I	36	-1960.6938	3999.0437	0.0000	1.0000
F81	38	-1987.9353	4058.1904	0.0000	1.0000
JC69	35	-2001.9997	4079.3384	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1868.3758	3824.7515	0.6414	0.6414
GTRIG	45	-1867.9586	3825.9171	0.3581	0.9995
GTRI	44	-1875.4437	3838.8875	0.0005	1.0000
HKYG	40	-1896.1274	3872.2548	0.0000	1.0000
HKYIG	41	-1895.7589	3873.5177	0.0000	1.0000
SYMG	41	-1895.7798	3873.5597	0.0000	1.0000
SYMIG	42	-1895.2978	3874.5957	0.0000	1.0000
HKYI	40	-1899.6813	3879.3626	0.0000	1.0000
SYMI	41	-1899.9602	3881.9204	0.0000	1.0000
K2PG	37	-1909.1991	3892.3982	0.0000	1.0000
K2PIG	38	-1908.8591	3893.7183	0.0000	1.0000
K2PI	37	-1912.6725	3899.3451	0.0000	1.0000
GTR	43	-1921.4634	3928.9268	0.0000	1.0000
HKY	39	-1942.9657	3963.9313	0.0000	1.0000
SYM	40	-1943.1563	3966.3125	0.0000	1.0000
F81G	39	-1944.2456	3966.4911	0.0000	1.0000
F81IG	40	-1944.0362	3968.0724	0.0000	1.0000
F81I	39	-1947.0825	3972.1649	0.0000	1.0000
K2P	36	-1955.3855	3982.7710	0.0000	1.0000
JC69G	36	-1958.2226	3988.4452	0.0000	1.0000
JC69IG	37	-1958.0955	3990.1910	0.0000	1.0000
JC69I	36	-1960.6938	3993.3876	0.0000	1.0000
F81	38	-1987.9353	4051.8706	0.0000	1.0000
JC69	35	-2001.9997	4073.9994	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1868.3758	4010.8927	0.9362	0.9362
GTRIG	45	-1867.9586	4016.2888	0.0630	0.9992
GTRI	44	-1875.4437	4025.0287	0.0008	1.0000
HKYG	40	-1896.1274	4041.4740	0.0000	1.0000
HKYIG	41	-1895.7589	4046.9675	0.0000	1.0000
SYMG	41	-1895.7798	4047.0094	0.0000	1.0000
HKYI	40	-1899.6813	4048.5818	0.0000	1.0000
K2PG	37	-1909.1991	4048.9260	0.0000	1.0000
SYMIG	42	-1895.2978	4052.2759	0.0000	1.0000
K2PIG	38	-1908.8591	4054.4766	0.0000	1.0000
SYMI	41	-1899.9602	4055.3701	0.0000	1.0000
K2PI	37	-1912.6725	4055.8729	0.0000	1.0000
GTR	43	-1921.4634	4110.8375	0.0000	1.0000
HKY	39	-1942.9657	4128.9201	0.0000	1.0000
F81G	39	-1944.2456	4131.4799	0.0000	1.0000
K2P	36	-1955.3855	4135.0684	0.0000	1.0000
SYM	40	-1943.1563	4135.5318	0.0000	1.0000
F81I	39	-1947.0825	4137.1537	0.0000	1.0000
F81IG	40	-1944.0362	4137.2916	0.0000	1.0000
JC69G	36	-1958.2226	4140.7425	0.0000	1.0000
JC69I	36	-1960.6938	4145.6849	0.0000	1.0000
JC69IG	37	-1958.0955	4146.7189	0.0000	1.0000
F81	38	-1987.9353	4212.6289	0.0000	1.0000
JC69	35	-2001.9997	4222.0663	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/chr6_9625.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9625.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/chr6_9625.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9625.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9625.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9625.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;


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End of Output

