
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:29 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/chr17_3088.phylip" (19 taxa, 1054 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: K2PIG


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
GTRIG	45	-3685.6175	7465.3421	0.9329	0.9329
GTRG	44	-3689.3491	7470.6229	0.0665	0.9995
SYMIG	42	-3697.0554	7481.6835	0.0003	0.9997
HKYIG	41	-3698.1624	7481.7279	0.0003	1.0000
SYMG	41	-3701.2564	7487.9160	0.0000	1.0000
HKYG	40	-3702.7598	7488.7575	0.0000	1.0000
K2PIG	38	-3704.9470	7488.8142	0.0000	1.0000
K2PG	37	-3709.9067	7496.5810	0.0000	1.0000
GTRI	44	-3703.2357	7498.3961	0.0000	1.0000
HKYI	40	-3709.5314	7502.3007	0.0000	1.0000
K2PI	37	-3716.8705	7510.5088	0.0000	1.0000
SYMI	41	-3715.7615	7516.9262	0.0000	1.0000
F81IG	40	-3770.0611	7623.3602	0.0000	1.0000
JC69IG	37	-3775.8165	7628.4008	0.0000	1.0000
F81G	39	-3773.9180	7628.9130	0.0000	1.0000
JC69G	36	-3779.8259	7634.2713	0.0000	1.0000
F81I	39	-3782.6938	7646.4646	0.0000	1.0000
JC69I	36	-3788.8902	7652.3998	0.0000	1.0000
GTR	43	-3816.6600	7723.0666	0.0000	1.0000
HKY	39	-3828.3255	7737.7279	0.0000	1.0000
SYM	40	-3831.3264	7745.8906	0.0000	1.0000
K2P	36	-3837.7692	7750.1579	0.0000	1.0000
F81	38	-3893.8794	7866.6791	0.0000	1.0000
JC69	35	-3901.6107	7875.6968	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3685.6175	7461.2350	0.9385	0.9385
GTRG	44	-3689.3491	7466.6982	0.0611	0.9996
SYMIG	42	-3697.0554	7478.1108	0.0002	0.9998
HKYIG	41	-3698.1624	7478.3248	0.0002	1.0000
SYMG	41	-3701.2564	7484.5129	0.0000	1.0000
HKYG	40	-3702.7598	7485.5196	0.0000	1.0000
K2PIG	38	-3704.9470	7485.8940	0.0000	1.0000
K2PG	37	-3709.9067	7493.8133	0.0000	1.0000
GTRI	44	-3703.2357	7494.4714	0.0000	1.0000
HKYI	40	-3709.5314	7499.0628	0.0000	1.0000
K2PI	37	-3716.8705	7507.7410	0.0000	1.0000
SYMI	41	-3715.7615	7513.5231	0.0000	1.0000
F81IG	40	-3770.0611	7620.1223	0.0000	1.0000
JC69IG	37	-3775.8165	7625.6331	0.0000	1.0000
F81G	39	-3773.9180	7625.8360	0.0000	1.0000
JC69G	36	-3779.8259	7631.6518	0.0000	1.0000
F81I	39	-3782.6938	7643.3876	0.0000	1.0000
JC69I	36	-3788.8902	7649.7804	0.0000	1.0000
GTR	43	-3816.6600	7719.3201	0.0000	1.0000
HKY	39	-3828.3255	7734.6510	0.0000	1.0000
SYM	40	-3831.3264	7742.6527	0.0000	1.0000
K2P	36	-3837.7692	7747.5385	0.0000	1.0000
F81	38	-3893.8794	7863.7589	0.0000	1.0000
JC69	35	-3901.6107	7873.2214	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PIG	38	-3704.9470	7674.3872	0.7828	0.7828
K2PG	37	-3709.9067	7677.3462	0.1783	0.9611
HKYIG	41	-3698.1624	7681.6990	0.0202	0.9813
HKYG	40	-3702.7598	7683.9335	0.0066	0.9879
GTRIG	45	-3685.6175	7684.4506	0.0051	0.9930
GTRG	44	-3689.3491	7684.9535	0.0040	0.9970
SYMIG	42	-3697.0554	7686.4454	0.0019	0.9989
SYMG	41	-3701.2564	7687.8871	0.0009	0.9998
K2PI	37	-3716.8705	7691.2739	0.0002	1.0000
HKYI	40	-3709.5314	7697.4767	0.0000	1.0000
GTRI	44	-3703.2357	7712.7267	0.0000	1.0000
SYMI	41	-3715.7615	7716.8973	0.0000	1.0000
JC69IG	37	-3775.8165	7809.1659	0.0000	1.0000
JC69G	36	-3779.8259	7810.2243	0.0000	1.0000
F81IG	40	-3770.0611	7818.5362	0.0000	1.0000
F81G	39	-3773.9180	7819.2896	0.0000	1.0000
JC69I	36	-3788.8902	7828.3529	0.0000	1.0000
F81I	39	-3782.6938	7836.8412	0.0000	1.0000
K2P	36	-3837.7692	7926.1110	0.0000	1.0000
HKY	39	-3828.3255	7928.1046	0.0000	1.0000
GTR	43	-3816.6600	7932.6150	0.0000	1.0000
SYM	40	-3831.3264	7941.0666	0.0000	1.0000
JC69	35	-3901.6107	8046.8335	0.0000	1.0000
F81	38	-3893.8794	8052.2521	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip = 1 - 1054;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip = 1 - 1054;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip = 1 - 1054;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3088.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


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

