
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:22 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/chrZ_495.phylip" (19 taxa, 709 characters)

Minimum AIC  model: GTRIG
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	-2468.6204	5031.2046	0.5276	0.5276
GTRIG	45	-2467.5908	5031.4259	0.4724	1.0000
HKYIG	41	-2483.8900	5054.9434	0.0000	1.0000
GTRI	44	-2480.8717	5055.7072	0.0000	1.0000
HKYG	40	-2485.6692	5056.2486	0.0000	1.0000
HKYI	40	-2495.1383	5075.1867	0.0000	1.0000
SYMIG	42	-2513.3422	5116.1078	0.0000	1.0000
SYMG	41	-2514.5776	5116.3187	0.0000	1.0000
K2PIG	38	-2519.1031	5118.6301	0.0000	1.0000
K2PG	37	-2520.6008	5119.3924	0.0000	1.0000
SYMI	41	-2522.7358	5132.6350	0.0000	1.0000
K2PI	37	-2528.8375	5135.8658	0.0000	1.0000
GTR	43	-2530.0018	5151.6938	0.0000	1.0000
HKY	39	-2542.9168	5168.4973	0.0000	1.0000
F81IG	40	-2557.4439	5199.7979	0.0000	1.0000
F81G	39	-2559.0126	5200.6889	0.0000	1.0000
F81I	39	-2565.7227	5214.1090	0.0000	1.0000
SYM	40	-2570.6084	5226.1270	0.0000	1.0000
K2P	36	-2576.0320	5228.0283	0.0000	1.0000
JC69G	36	-2589.8445	5255.6533	0.0000	1.0000
JC69IG	37	-2588.8430	5255.8768	0.0000	1.0000
JC69I	36	-2597.0314	5270.0270	0.0000	1.0000
F81	38	-2609.0727	5298.5693	0.0000	1.0000
JC69	35	-2638.6347	5351.0137	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2467.5908	5025.1816	0.5074	0.5074
GTRG	44	-2468.6204	5025.2407	0.4926	1.0000
GTRI	44	-2480.8717	5049.7434	0.0000	1.0000
HKYIG	41	-2483.8900	5049.7800	0.0000	1.0000
HKYG	40	-2485.6692	5051.3384	0.0000	1.0000
HKYI	40	-2495.1383	5070.2765	0.0000	1.0000
SYMIG	42	-2513.3422	5110.6844	0.0000	1.0000
SYMG	41	-2514.5776	5111.1552	0.0000	1.0000
K2PIG	38	-2519.1031	5114.2062	0.0000	1.0000
K2PG	37	-2520.6008	5115.2017	0.0000	1.0000
SYMI	41	-2522.7358	5127.4716	0.0000	1.0000
K2PI	37	-2528.8375	5131.6750	0.0000	1.0000
GTR	43	-2530.0018	5146.0036	0.0000	1.0000
HKY	39	-2542.9168	5163.8336	0.0000	1.0000
F81IG	40	-2557.4439	5194.8877	0.0000	1.0000
F81G	39	-2559.0126	5196.0252	0.0000	1.0000
F81I	39	-2565.7227	5209.4453	0.0000	1.0000
SYM	40	-2570.6084	5221.2168	0.0000	1.0000
K2P	36	-2576.0320	5224.0640	0.0000	1.0000
JC69IG	37	-2588.8430	5251.6861	0.0000	1.0000
JC69G	36	-2589.8445	5251.6890	0.0000	1.0000
JC69I	36	-2597.0314	5266.0627	0.0000	1.0000
F81	38	-2609.0727	5294.1454	0.0000	1.0000
JC69	35	-2638.6347	5347.2693	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-2468.6204	5226.0503	0.8854	0.8854
GTRIG	45	-2467.5908	5230.5551	0.0931	0.9785
HKYG	40	-2485.6692	5233.8926	0.0175	0.9961
HKYIG	41	-2483.8900	5236.8980	0.0039	1.0000
GTRI	44	-2480.8717	5250.5530	0.0000	1.0000
HKYI	40	-2495.1383	5252.8307	0.0000	1.0000
K2PG	37	-2520.6008	5284.0643	0.0000	1.0000
K2PIG	38	-2519.1031	5287.6327	0.0000	1.0000
SYMG	41	-2514.5776	5298.2733	0.0000	1.0000
K2PI	37	-2528.8375	5300.5377	0.0000	1.0000
SYMIG	42	-2513.3422	5302.3663	0.0000	1.0000
SYMI	41	-2522.7358	5314.5897	0.0000	1.0000
HKY	39	-2542.9168	5341.8240	0.0000	1.0000
GTR	43	-2530.0018	5342.2494	0.0000	1.0000
F81G	39	-2559.0126	5374.0156	0.0000	1.0000
F81IG	40	-2557.4439	5377.4420	0.0000	1.0000
F81I	39	-2565.7227	5387.4357	0.0000	1.0000
K2P	36	-2576.0320	5388.3628	0.0000	1.0000
SYM	40	-2570.6084	5403.7710	0.0000	1.0000
JC69G	36	-2589.8445	5415.9878	0.0000	1.0000
JC69IG	37	-2588.8430	5420.5487	0.0000	1.0000
JC69I	36	-2597.0314	5430.3615	0.0000	1.0000
F81	38	-2609.0727	5467.5720	0.0000	1.0000
JC69	35	-2638.6347	5507.0043	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/chrZ_495.phylip = 1 - 709;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_495.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_495.phylip = 1 - 709;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_495.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/chrZ_495.phylip = 1 - 709;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_495.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

