
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:02 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/chr18_4493.phylip" (19 taxa, 980 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	-2712.5621	5517.3595	0.5121	0.5121
GTRIG	45	-2711.6833	5517.7991	0.4111	0.9232
GTRI	44	-2714.9646	5522.1645	0.0463	0.9695
HKYG	40	-2720.4049	5524.3030	0.0159	0.9854
HKYIG	41	-2719.5992	5524.8700	0.0120	0.9974
HKYI	40	-2722.2197	5527.9325	0.0026	1.0000
F81G	39	-2739.0880	5559.4952	0.0000	1.0000
F81IG	40	-2738.4001	5560.2932	0.0000	1.0000
F81I	39	-2740.9198	5563.1587	0.0000	1.0000
GTR	43	-2749.5153	5589.0734	0.0000	1.0000
HKY	39	-2760.4207	5602.1605	0.0000	1.0000
F81	38	-2776.0933	5631.3365	0.0000	1.0000
SYMG	41	-2790.0803	5665.8322	0.0000	1.0000
SYMIG	42	-2789.4101	5666.6750	0.0000	1.0000
SYMI	41	-2792.4344	5670.5405	0.0000	1.0000
K2PG	37	-2798.7064	5674.3979	0.0000	1.0000
K2PIG	38	-2798.0126	5675.1750	0.0000	1.0000
K2PI	37	-2800.5267	5678.0385	0.0000	1.0000
JC69G	36	-2810.9574	5696.7398	0.0000	1.0000
JC69IG	37	-2810.3029	5697.5910	0.0000	1.0000
JC69I	36	-2812.7496	5700.3242	0.0000	1.0000
SYM	40	-2822.7415	5728.9760	0.0000	1.0000
K2P	36	-2834.8550	5744.5350	0.0000	1.0000
JC69	35	-2846.5554	5765.7802	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2712.5621	5513.1242	0.4953	0.4953
GTRIG	45	-2711.6833	5513.3665	0.4388	0.9341
GTRI	44	-2714.9646	5517.9292	0.0448	0.9789
HKYG	40	-2720.4049	5520.8099	0.0106	0.9895
HKYIG	41	-2719.5992	5521.1983	0.0087	0.9983
HKYI	40	-2722.2197	5524.4394	0.0017	1.0000
F81G	39	-2739.0880	5556.1760	0.0000	1.0000
F81IG	40	-2738.4001	5556.8001	0.0000	1.0000
F81I	39	-2740.9198	5559.8395	0.0000	1.0000
GTR	43	-2749.5153	5585.0306	0.0000	1.0000
HKY	39	-2760.4207	5598.8414	0.0000	1.0000
F81	38	-2776.0933	5628.1866	0.0000	1.0000
SYMG	41	-2790.0803	5662.1606	0.0000	1.0000
SYMIG	42	-2789.4101	5662.8201	0.0000	1.0000
SYMI	41	-2792.4344	5666.8689	0.0000	1.0000
K2PG	37	-2798.7064	5671.4128	0.0000	1.0000
K2PIG	38	-2798.0126	5672.0252	0.0000	1.0000
K2PI	37	-2800.5267	5675.0534	0.0000	1.0000
JC69G	36	-2810.9574	5693.9147	0.0000	1.0000
JC69IG	37	-2810.3029	5694.6058	0.0000	1.0000
JC69I	36	-2812.7496	5697.4992	0.0000	1.0000
SYM	40	-2822.7415	5725.4830	0.0000	1.0000
K2P	36	-2834.8550	5741.7099	0.0000	1.0000
JC69	35	-2846.5554	5763.1107	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2720.4049	5716.3120	0.8081	0.8081
HKYI	40	-2722.2197	5719.9415	0.1316	0.9397
HKYIG	41	-2719.5992	5721.5880	0.0578	0.9975
GTRG	44	-2712.5621	5728.1765	0.0021	0.9996
GTRI	44	-2714.9646	5732.9816	0.0002	0.9998
GTRIG	45	-2711.6833	5733.3064	0.0002	1.0000
F81G	39	-2739.0880	5746.7906	0.0000	1.0000
F81I	39	-2740.9198	5750.4541	0.0000	1.0000
F81IG	40	-2738.4001	5752.3022	0.0000	1.0000
HKY	39	-2760.4207	5789.4559	0.0000	1.0000
GTR	43	-2749.5153	5795.1954	0.0000	1.0000
F81	38	-2776.0933	5813.9136	0.0000	1.0000
K2PG	37	-2798.7064	5852.2522	0.0000	1.0000
K2PI	37	-2800.5267	5855.8928	0.0000	1.0000
K2PIG	38	-2798.0126	5857.7522	0.0000	1.0000
SYMG	41	-2790.0803	5862.5502	0.0000	1.0000
SYMI	41	-2792.4344	5867.2585	0.0000	1.0000
SYMIG	42	-2789.4101	5868.0973	0.0000	1.0000
JC69G	36	-2810.9574	5869.8666	0.0000	1.0000
JC69I	36	-2812.7496	5873.4511	0.0000	1.0000
JC69IG	37	-2810.3029	5875.4453	0.0000	1.0000
K2P	36	-2834.8550	5917.6618	0.0000	1.0000
SYM	40	-2822.7415	5920.9851	0.0000	1.0000
JC69	35	-2846.5554	5934.1750	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/chr18_4493.phylip = 1 - 980;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_4493.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/chr18_4493.phylip = 1 - 980;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_4493.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/chr18_4493.phylip = 1 - 980;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_4493.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

