
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:38 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/chr12_5983.phylip" (19 taxa, 784 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	-2367.2067	4830.0232	0.7908	0.7908
GTRG	44	-2369.9242	4833.2069	0.1610	0.9518
HKYIG	41	-2374.7926	4836.2267	0.0356	0.9873
HKYG	40	-2377.1660	4838.7465	0.0101	0.9974
GTRI	44	-2374.1986	4841.7558	0.0022	0.9997
HKYI	40	-2380.5418	4845.4982	0.0003	1.0000
K2PIG	38	-2407.7141	4895.4066	0.0000	1.0000
K2PG	37	-2409.4991	4896.7677	0.0000	1.0000
SYMIG	42	-2404.9359	4898.7462	0.0000	1.0000
SYMG	41	-2406.6549	4899.9514	0.0000	1.0000
K2PI	37	-2411.7131	4901.1957	0.0000	1.0000
SYMI	41	-2408.8010	4904.2435	0.0000	1.0000
F81IG	40	-2425.9486	4936.3118	0.0000	1.0000
F81G	39	-2427.7611	4937.7157	0.0000	1.0000
F81I	39	-2430.2212	4942.6360	0.0000	1.0000
GTR	43	-2430.3166	4951.7467	0.0000	1.0000
HKY	39	-2437.6706	4957.5348	0.0000	1.0000
JC69IG	37	-2452.9773	4983.7240	0.0000	1.0000
JC69G	36	-2454.4705	4984.5072	0.0000	1.0000
JC69I	36	-2456.4774	4988.5212	0.0000	1.0000
K2P	36	-2470.4918	5016.5499	0.0000	1.0000
SYM	40	-2466.5440	5017.5026	0.0000	1.0000
F81	38	-2485.0796	5050.1378	0.0000	1.0000
JC69	35	-2512.1029	5097.5748	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2367.2067	4824.4134	0.8217	0.8217
GTRG	44	-2369.9242	4827.8483	0.1475	0.9692
HKYIG	41	-2374.7926	4831.5852	0.0228	0.9920
HKYG	40	-2377.1660	4834.3320	0.0058	0.9977
GTRI	44	-2374.1986	4836.3972	0.0021	0.9998
HKYI	40	-2380.5418	4841.0836	0.0002	1.0000
K2PIG	38	-2407.7141	4891.4281	0.0000	1.0000
K2PG	37	-2409.4991	4892.9983	0.0000	1.0000
SYMIG	42	-2404.9359	4893.8717	0.0000	1.0000
SYMG	41	-2406.6549	4895.3099	0.0000	1.0000
K2PI	37	-2411.7131	4897.4262	0.0000	1.0000
SYMI	41	-2408.8010	4899.6020	0.0000	1.0000
F81IG	40	-2425.9486	4931.8973	0.0000	1.0000
F81G	39	-2427.7611	4933.5222	0.0000	1.0000
F81I	39	-2430.2212	4938.4425	0.0000	1.0000
GTR	43	-2430.3166	4946.6331	0.0000	1.0000
HKY	39	-2437.6706	4953.3413	0.0000	1.0000
JC69IG	37	-2452.9773	4979.9546	0.0000	1.0000
JC69G	36	-2454.4705	4980.9410	0.0000	1.0000
JC69I	36	-2456.4774	4984.9549	0.0000	1.0000
K2P	36	-2470.4918	5012.9837	0.0000	1.0000
SYM	40	-2466.5440	5013.0881	0.0000	1.0000
F81	38	-2485.0796	5046.1593	0.0000	1.0000
JC69	35	-2512.1029	5094.2058	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2377.1660	5020.9083	0.7037	0.7037
HKYIG	41	-2374.7926	5022.8260	0.2698	0.9735
HKYI	40	-2380.5418	5027.6600	0.0241	0.9975
GTRG	44	-2369.9242	5033.0823	0.0016	0.9991
GTRIG	45	-2367.2067	5034.3118	0.0009	1.0000
GTRI	44	-2374.1986	5041.6312	0.0000	1.0000
K2PG	37	-2409.4991	5065.5814	0.0000	1.0000
K2PIG	38	-2407.7141	5068.6756	0.0000	1.0000
K2PI	37	-2411.7131	5070.0094	0.0000	1.0000
SYMG	41	-2406.6549	5086.5506	0.0000	1.0000
SYMIG	42	-2404.9359	5089.7769	0.0000	1.0000
SYMI	41	-2408.8010	5090.8428	0.0000	1.0000
F81G	39	-2427.7611	5115.4342	0.0000	1.0000
F81IG	40	-2425.9486	5118.4736	0.0000	1.0000
F81I	39	-2430.2212	5120.3544	0.0000	1.0000
HKY	39	-2437.6706	5135.2532	0.0000	1.0000
GTR	43	-2430.3166	5147.2027	0.0000	1.0000
JC69G	36	-2454.4705	5148.8597	0.0000	1.0000
JC69IG	37	-2452.9773	5152.5377	0.0000	1.0000
JC69I	36	-2456.4774	5152.8736	0.0000	1.0000
K2P	36	-2470.4918	5180.9024	0.0000	1.0000
SYM	40	-2466.5440	5199.6645	0.0000	1.0000
F81	38	-2485.0796	5223.4068	0.0000	1.0000
JC69	35	-2512.1029	5257.4601	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/chr12_5983.phylip = 1 - 784;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5983.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/chr12_5983.phylip = 1 - 784;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5983.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/chr12_5983.phylip = 1 - 784;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5983.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

