
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:56 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/chr2_23548.phylip" (19 taxa, 557 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	-1660.8164	3417.3671	0.4632	0.4632
GTRI	44	-1661.3518	3418.4379	0.2712	0.7344
GTRIG	45	-1660.2014	3418.5045	0.2623	0.9967
HKYG	40	-1671.2728	3428.9022	0.0014	0.9981
HKYI	40	-1671.5158	3429.3882	0.0011	0.9993
HKYIG	41	-1670.8102	3430.3078	0.0007	1.0000
K2PG	37	-1685.6497	3450.7176	0.0000	1.0000
K2PI	37	-1685.8280	3451.0741	0.0000	1.0000
K2PIG	38	-1685.2373	3452.1967	0.0000	1.0000
SYMG	41	-1682.0603	3452.8080	0.0000	1.0000
SYMI	41	-1682.2084	3453.1042	0.0000	1.0000
SYMIG	42	-1681.5554	3454.1380	0.0000	1.0000
GTR	43	-1689.9423	3473.2609	0.0000	1.0000
HKY	39	-1701.6755	3487.3859	0.0000	1.0000
F81G	39	-1711.6144	3507.2635	0.0000	1.0000
F81I	39	-1711.6730	3507.3808	0.0000	1.0000
F81IG	40	-1711.1709	3508.6983	0.0000	1.0000
SYM	40	-1713.7863	3513.9291	0.0000	1.0000
K2P	36	-1718.4381	3513.9993	0.0000	1.0000
JC69G	36	-1724.4588	3526.0407	0.0000	1.0000
JC69I	36	-1724.5378	3526.1987	0.0000	1.0000
JC69IG	37	-1724.0436	3527.5053	0.0000	1.0000
F81	38	-1741.3538	3564.4296	0.0000	1.0000
JC69	35	-1755.4623	3585.7615	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1660.8164	3409.6327	0.4406	0.4406
GTRIG	45	-1660.2014	3410.4028	0.2998	0.7404
GTRI	44	-1661.3518	3410.7035	0.2579	0.9984
HKYG	40	-1671.2728	3422.5456	0.0007	0.9991
HKYI	40	-1671.5158	3423.0316	0.0005	0.9996
HKYIG	41	-1670.8102	3423.6205	0.0004	1.0000
K2PG	37	-1685.6497	3445.2994	0.0000	1.0000
K2PI	37	-1685.8280	3445.6560	0.0000	1.0000
SYMG	41	-1682.0603	3446.1206	0.0000	1.0000
SYMI	41	-1682.2084	3446.4168	0.0000	1.0000
K2PIG	38	-1685.2373	3446.4747	0.0000	1.0000
SYMIG	42	-1681.5554	3447.1108	0.0000	1.0000
GTR	43	-1689.9423	3465.8847	0.0000	1.0000
HKY	39	-1701.6755	3481.3511	0.0000	1.0000
F81G	39	-1711.6144	3501.2287	0.0000	1.0000
F81I	39	-1711.6730	3501.3460	0.0000	1.0000
F81IG	40	-1711.1709	3502.3418	0.0000	1.0000
SYM	40	-1713.7863	3507.5726	0.0000	1.0000
K2P	36	-1718.4381	3508.8762	0.0000	1.0000
JC69G	36	-1724.4588	3520.9176	0.0000	1.0000
JC69I	36	-1724.5378	3521.0757	0.0000	1.0000
JC69IG	37	-1724.0436	3522.0872	0.0000	1.0000
F81	38	-1741.3538	3558.7076	0.0000	1.0000
JC69	35	-1755.4623	3580.9246	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1671.2728	3595.4482	0.4873	0.4873
HKYI	40	-1671.5158	3595.9342	0.3822	0.8694
GTRG	44	-1660.8164	3599.8256	0.0546	0.9240
HKYIG	41	-1670.8102	3600.8456	0.0328	0.9568
GTRI	44	-1661.3518	3600.8964	0.0320	0.9888
GTRIG	45	-1660.2014	3604.9182	0.0043	0.9931
K2PG	37	-1685.6497	3605.2344	0.0037	0.9967
K2PI	37	-1685.8280	3605.5909	0.0031	0.9998
K2PIG	38	-1685.2373	3610.7322	0.0002	1.0000
SYMG	41	-1682.0603	3623.3458	0.0000	1.0000
SYMI	41	-1682.2084	3623.6420	0.0000	1.0000
SYMIG	42	-1681.5554	3628.6585	0.0000	1.0000
HKY	39	-1701.6755	3649.9311	0.0000	1.0000
GTR	43	-1689.9423	3651.7550	0.0000	1.0000
K2P	36	-1718.4381	3664.4885	0.0000	1.0000
F81G	39	-1711.6144	3669.8088	0.0000	1.0000
F81I	39	-1711.6730	3669.9261	0.0000	1.0000
F81IG	40	-1711.1709	3675.2444	0.0000	1.0000
JC69G	36	-1724.4588	3676.5300	0.0000	1.0000
JC69I	36	-1724.5378	3676.6880	0.0000	1.0000
SYM	40	-1713.7863	3680.4752	0.0000	1.0000
JC69IG	37	-1724.0436	3682.0221	0.0000	1.0000
F81	38	-1741.3538	3722.9651	0.0000	1.0000
JC69	35	-1755.4623	3732.2144	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/chr2_23548.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23548.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/chr2_23548.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23548.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/chr2_23548.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23548.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

