
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:57 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_23600.phylip" (19 taxa, 677 characters)

Minimum AIC  model: GTRG
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	-2353.1170	4791.3913	0.3811	0.3811
GTRG	44	-2348.9343	4792.1344	0.2628	0.6439
HKYIG	41	-2353.0866	4793.5968	0.1265	0.7704
HKYI	40	-2354.5034	4794.1640	0.0953	0.8657
GTRIG	45	-2348.9191	4794.3992	0.0847	0.9504
GTRI	44	-2350.6017	4795.4692	0.0496	1.0000
HKY	39	-2373.5325	4829.9630	0.0000	1.0000
GTR	43	-2369.5737	4831.1254	0.0000	1.0000
K2PG	37	-2380.8489	4840.0985	0.0000	1.0000
K2PIG	38	-2380.7964	4842.2385	0.0000	1.0000
K2PI	37	-2381.9549	4842.3105	0.0000	1.0000
SYMG	41	-2379.7909	4847.0054	0.0000	1.0000
SYMIG	42	-2379.7538	4849.2047	0.0000	1.0000
SYMI	41	-2380.9520	4849.3276	0.0000	1.0000
K2P	36	-2402.8569	4881.8762	0.0000	1.0000
SYM	40	-2401.6394	4888.4361	0.0000	1.0000
F81G	39	-2414.4289	4911.7557	0.0000	1.0000
F81I	39	-2415.4016	4913.7012	0.0000	1.0000
F81IG	40	-2414.3860	4913.9293	0.0000	1.0000
F81	38	-2434.2480	4949.1417	0.0000	1.0000
JC69G	36	-2437.3736	4950.9098	0.0000	1.0000
JC69I	36	-2438.2824	4952.7273	0.0000	1.0000
JC69IG	37	-2437.3098	4953.0203	0.0000	1.0000
JC69	35	-2457.9478	4989.8270	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2348.9343	4785.8685	0.3425	0.3425
HKYG	40	-2353.1170	4786.2340	0.2853	0.6279
GTRIG	45	-2348.9191	4787.8382	0.1279	0.7558
HKYIG	41	-2353.0866	4788.1731	0.1082	0.8640
HKYI	40	-2354.5034	4789.0068	0.0713	0.9354
GTRI	44	-2350.6017	4789.2034	0.0646	1.0000
HKY	39	-2373.5325	4825.0650	0.0000	1.0000
GTR	43	-2369.5737	4825.1475	0.0000	1.0000
K2PG	37	-2380.8489	4835.6979	0.0000	1.0000
K2PIG	38	-2380.7964	4837.5928	0.0000	1.0000
K2PI	37	-2381.9549	4837.9098	0.0000	1.0000
SYMG	41	-2379.7909	4841.5818	0.0000	1.0000
SYMIG	42	-2379.7538	4843.5076	0.0000	1.0000
SYMI	41	-2380.9520	4843.9039	0.0000	1.0000
K2P	36	-2402.8569	4877.7137	0.0000	1.0000
SYM	40	-2401.6394	4883.2789	0.0000	1.0000
F81G	39	-2414.4289	4906.8577	0.0000	1.0000
F81IG	40	-2414.3860	4908.7721	0.0000	1.0000
F81I	39	-2415.4016	4908.8032	0.0000	1.0000
F81	38	-2434.2480	4944.4960	0.0000	1.0000
JC69G	36	-2437.3736	4946.7473	0.0000	1.0000
JC69I	36	-2438.2824	4948.5648	0.0000	1.0000
JC69IG	37	-2437.3098	4948.6197	0.0000	1.0000
JC69	35	-2457.9478	4985.8956	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2353.1170	4966.9409	0.7753	0.7753
HKYI	40	-2354.5034	4969.7136	0.1938	0.9691
HKYIG	41	-2353.0866	4973.3977	0.0307	0.9999
GTRG	44	-2348.9343	4984.6461	0.0001	1.0000
GTRI	44	-2350.6017	4987.9810	0.0000	1.0000
GTRIG	45	-2348.9191	4991.1334	0.0000	1.0000
HKY	39	-2373.5325	5001.2542	0.0000	1.0000
K2PG	37	-2380.8489	5002.8517	0.0000	1.0000
K2PI	37	-2381.9549	5005.0637	0.0000	1.0000
K2PIG	38	-2380.7964	5009.2643	0.0000	1.0000
GTR	43	-2369.5737	5019.4073	0.0000	1.0000
SYMG	41	-2379.7909	5026.8063	0.0000	1.0000
SYMI	41	-2380.9520	5029.1285	0.0000	1.0000
SYMIG	42	-2379.7538	5033.2498	0.0000	1.0000
K2P	36	-2402.8569	5040.3499	0.0000	1.0000
SYM	40	-2401.6394	5063.9857	0.0000	1.0000
F81G	39	-2414.4289	5083.0469	0.0000	1.0000
F81I	39	-2415.4016	5084.9924	0.0000	1.0000
F81IG	40	-2414.3860	5089.4789	0.0000	1.0000
JC69G	36	-2437.3736	5109.3835	0.0000	1.0000
JC69I	36	-2438.2824	5111.2010	0.0000	1.0000
JC69IG	37	-2437.3098	5115.7735	0.0000	1.0000
F81	38	-2434.2480	5116.1675	0.0000	1.0000
JC69	35	-2457.9478	5144.0141	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_23600.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23600.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23600.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23600.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/chr2_23600.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23600.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

