
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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/chr13_2821.phylip" (19 taxa, 716 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2289.9169	4676.0128	0.3884	0.3884
GTRG	44	-2291.1704	4676.2424	0.3463	0.7347
HKYIG	41	-2295.4673	4678.0444	0.1407	0.8754
HKYG	40	-2296.7789	4678.4171	0.1167	0.9921
GTRI	44	-2295.4805	4684.8627	0.0047	0.9967
HKYI	40	-2300.3599	4685.5791	0.0033	1.0000
K2PIG	38	-2321.5200	4723.4181	0.0000	1.0000
K2PG	37	-2322.8544	4723.8562	0.0000	1.0000
SYMIG	42	-2320.1720	4729.7111	0.0000	1.0000
K2PI	37	-2325.7843	4729.7160	0.0000	1.0000
SYMG	41	-2321.4718	4730.0534	0.0000	1.0000
SYMI	41	-2324.3678	4735.8455	0.0000	1.0000
GTR	43	-2342.8565	4777.3440	0.0000	1.0000
HKY	39	-2350.0799	4782.7752	0.0000	1.0000
K2P	36	-2379.2581	4834.4396	0.0000	1.0000
SYM	40	-2377.3398	4839.5388	0.0000	1.0000
F81G	39	-2381.6576	4845.9306	0.0000	1.0000
F81IG	40	-2380.7456	4846.3505	0.0000	1.0000
F81I	39	-2384.4199	4851.4552	0.0000	1.0000
JC69G	36	-2403.1862	4882.2958	0.0000	1.0000
JC69IG	37	-2402.2182	4882.5839	0.0000	1.0000
JC69I	36	-2405.7927	4887.5088	0.0000	1.0000
F81	38	-2432.7352	4945.8486	0.0000	1.0000
JC69	35	-2456.3318	4986.3695	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2289.9169	4669.8337	0.4633	0.4633
GTRG	44	-2291.1704	4670.3408	0.3596	0.8229
HKYIG	41	-2295.4673	4672.9346	0.0983	0.9212
HKYG	40	-2296.7789	4673.5578	0.0720	0.9932
GTRI	44	-2295.4805	4678.9611	0.0048	0.9980
HKYI	40	-2300.3599	4680.7199	0.0020	1.0000
K2PIG	38	-2321.5200	4719.0399	0.0000	1.0000
K2PG	37	-2322.8544	4719.7087	0.0000	1.0000
SYMIG	42	-2320.1720	4724.3440	0.0000	1.0000
SYMG	41	-2321.4718	4724.9436	0.0000	1.0000
K2PI	37	-2325.7843	4725.5685	0.0000	1.0000
SYMI	41	-2324.3678	4730.7357	0.0000	1.0000
GTR	43	-2342.8565	4771.7130	0.0000	1.0000
HKY	39	-2350.0799	4778.1598	0.0000	1.0000
K2P	36	-2379.2581	4830.5162	0.0000	1.0000
SYM	40	-2377.3398	4834.6796	0.0000	1.0000
F81G	39	-2381.6576	4841.3153	0.0000	1.0000
F81IG	40	-2380.7456	4841.4912	0.0000	1.0000
F81I	39	-2384.4199	4846.8399	0.0000	1.0000
JC69G	36	-2403.1862	4878.3724	0.0000	1.0000
JC69IG	37	-2402.2182	4878.4364	0.0000	1.0000
JC69I	36	-2405.7927	4883.5854	0.0000	1.0000
F81	38	-2432.7352	4941.4705	0.0000	1.0000
JC69	35	-2456.3318	4982.6637	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2296.7789	4856.5050	0.8568	0.8568
HKYIG	41	-2295.4673	4860.4555	0.1189	0.9756
HKYI	40	-2300.3599	4863.6671	0.0239	0.9995
GTRG	44	-2291.1704	4871.5827	0.0005	0.9999
GTRIG	45	-2289.9169	4875.6493	0.0001	1.0000
GTRI	44	-2295.4805	4880.2030	0.0000	1.0000
K2PG	37	-2322.8544	4888.9349	0.0000	1.0000
K2PIG	38	-2321.5200	4892.8398	0.0000	1.0000
K2PI	37	-2325.7843	4894.7947	0.0000	1.0000
SYMG	41	-2321.4718	4912.4645	0.0000	1.0000
SYMIG	42	-2320.1720	4916.4386	0.0000	1.0000
SYMI	41	-2324.3678	4918.2566	0.0000	1.0000
HKY	39	-2350.0799	4956.5333	0.0000	1.0000
GTR	43	-2342.8565	4968.3813	0.0000	1.0000
K2P	36	-2379.2581	4995.1687	0.0000	1.0000
SYM	40	-2377.3398	5017.6268	0.0000	1.0000
F81G	39	-2381.6576	5019.6888	0.0000	1.0000
F81IG	40	-2380.7456	5024.4384	0.0000	1.0000
F81I	39	-2384.4199	5025.2134	0.0000	1.0000
JC69G	36	-2403.1862	5043.0249	0.0000	1.0000
JC69IG	37	-2402.2182	5047.6626	0.0000	1.0000
JC69I	36	-2405.7927	5048.2379	0.0000	1.0000
F81	38	-2432.7352	5115.2703	0.0000	1.0000
JC69	35	-2456.3318	5142.7425	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/chr13_2821.phylip = 1 - 716;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2821.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/chr13_2821.phylip = 1 - 716;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2821.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2821.phylip = 1 - 716;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2821.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

