
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:37 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/chr1_8696.phylip" (19 taxa, 625 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2480.9412	5047.4988	0.6246	0.6246
HKYIG	41	-2480.4921	5048.8916	0.3113	0.9359
GTRG	44	-2479.0086	5052.8448	0.0431	0.9790
GTRIG	45	-2478.7977	5054.7456	0.0167	0.9957
HKYI	40	-2485.9506	5057.5176	0.0042	0.9998
GTRI	44	-2484.5250	5063.8776	0.0002	1.0000
K2PG	37	-2505.0941	5088.9786	0.0000	1.0000
K2PIG	38	-2504.8030	5090.6640	0.0000	1.0000
SYMG	41	-2504.0093	5095.9260	0.0000	1.0000
SYMIG	42	-2503.7039	5097.6140	0.0000	1.0000
K2PI	37	-2509.8502	5098.4908	0.0000	1.0000
SYMI	41	-2508.3366	5104.5806	0.0000	1.0000
HKY	39	-2533.9333	5151.2000	0.0000	1.0000
GTR	43	-2532.9828	5158.4785	0.0000	1.0000
F81G	39	-2539.0583	5161.4499	0.0000	1.0000
F81IG	40	-2538.8561	5163.3286	0.0000	1.0000
F81I	39	-2543.9814	5171.2961	0.0000	1.0000
JC69G	36	-2558.2117	5192.9539	0.0000	1.0000
K2P	36	-2558.3759	5193.2824	0.0000	1.0000
JC69IG	37	-2557.9996	5194.7896	0.0000	1.0000
SYM	40	-2557.6387	5200.8938	0.0000	1.0000
JC69I	36	-2563.1192	5202.7690	0.0000	1.0000
F81	38	-2590.5482	5262.1545	0.0000	1.0000
JC69	35	-2609.9013	5294.0811	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2480.9412	5041.8823	0.5658	0.5658
HKYIG	41	-2480.4921	5042.9842	0.3261	0.8919
GTRG	44	-2479.0086	5046.0172	0.0716	0.9634
GTRIG	45	-2478.7977	5047.5954	0.0325	0.9959
HKYI	40	-2485.9506	5051.9011	0.0038	0.9997
GTRI	44	-2484.5250	5057.0500	0.0003	1.0000
K2PG	37	-2505.0941	5084.1882	0.0000	1.0000
K2PIG	38	-2504.8030	5085.6060	0.0000	1.0000
SYMG	41	-2504.0093	5090.0187	0.0000	1.0000
SYMIG	42	-2503.7039	5091.4078	0.0000	1.0000
K2PI	37	-2509.8502	5093.7003	0.0000	1.0000
SYMI	41	-2508.3366	5098.6732	0.0000	1.0000
HKY	39	-2533.9333	5145.8667	0.0000	1.0000
GTR	43	-2532.9828	5151.9656	0.0000	1.0000
F81G	39	-2539.0583	5156.1165	0.0000	1.0000
F81IG	40	-2538.8561	5157.7122	0.0000	1.0000
F81I	39	-2543.9814	5165.9628	0.0000	1.0000
JC69G	36	-2558.2117	5188.4233	0.0000	1.0000
K2P	36	-2558.3759	5188.7517	0.0000	1.0000
JC69IG	37	-2557.9996	5189.9992	0.0000	1.0000
SYM	40	-2557.6387	5195.2773	0.0000	1.0000
JC69I	36	-2563.1192	5198.2383	0.0000	1.0000
F81	38	-2590.5482	5257.0964	0.0000	1.0000
JC69	35	-2609.9013	5289.8027	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2480.9412	5219.3924	0.9351	0.9351
HKYIG	41	-2480.4921	5224.9321	0.0586	0.9937
HKYI	40	-2485.9506	5229.4112	0.0062	1.0000
GTRG	44	-2479.0086	5241.2783	0.0000	1.0000
GTRIG	45	-2478.7977	5247.2942	0.0000	1.0000
K2PG	37	-2505.0941	5248.3850	0.0000	1.0000
GTRI	44	-2484.5250	5252.3111	0.0000	1.0000
K2PIG	38	-2504.8030	5254.2406	0.0000	1.0000
K2PI	37	-2509.8502	5257.8971	0.0000	1.0000
SYMG	41	-2504.0093	5271.9665	0.0000	1.0000
SYMIG	42	-2503.7039	5277.7934	0.0000	1.0000
SYMI	41	-2508.3366	5280.6210	0.0000	1.0000
HKY	39	-2533.9333	5318.9390	0.0000	1.0000
F81G	39	-2539.0583	5329.1888	0.0000	1.0000
F81IG	40	-2538.8561	5335.2222	0.0000	1.0000
F81I	39	-2543.9814	5339.0351	0.0000	1.0000
GTR	43	-2532.9828	5342.7890	0.0000	1.0000
JC69G	36	-2558.2117	5348.1824	0.0000	1.0000
K2P	36	-2558.3759	5348.5108	0.0000	1.0000
JC69IG	37	-2557.9996	5354.1960	0.0000	1.0000
JC69I	36	-2563.1192	5357.9974	0.0000	1.0000
SYM	40	-2557.6387	5372.7874	0.0000	1.0000
F81	38	-2590.5482	5425.7310	0.0000	1.0000
JC69	35	-2609.9013	5445.1240	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8696.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8696.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;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8696.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8696.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;


[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/chr1_8696.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8696.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

