
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:21 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/chr3_6231.phylip" (19 taxa, 796 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	-2465.8510	5016.0463	0.3534	0.3534
GTRG	44	-2461.4686	5016.2101	0.3256	0.6790
HKYI	40	-2466.3514	5017.0471	0.2143	0.8933
HKYIG	41	-2465.9707	5018.5090	0.1032	0.9965
GTRIG	45	-2465.4771	5026.4743	0.0019	0.9984
GTRI	44	-2467.0503	5027.3735	0.0012	0.9996
K2PG	37	-2476.6586	5031.0270	0.0002	0.9998
K2PI	37	-2477.1820	5032.0738	0.0001	0.9999
K2PIG	38	-2476.7688	5033.4531	0.0001	1.0000
SYMG	41	-2479.6414	5045.8504	0.0000	1.0000
SYMIG	42	-2479.3927	5047.5823	0.0000	1.0000
SYMI	41	-2480.7573	5048.0823	0.0000	1.0000
F81G	39	-2520.4967	5123.1204	0.0000	1.0000
HKY	39	-2522.5673	5127.2616	0.0000	1.0000
F81IG	40	-2522.1607	5128.6658	0.0000	1.0000
F81I	39	-2523.5430	5129.2130	0.0000	1.0000
GTR	43	-2520.4994	5132.0308	0.0000	1.0000
JC69G	36	-2528.7808	5133.0715	0.0000	1.0000
JC69IG	37	-2530.9107	5139.5311	0.0000	1.0000
JC69I	36	-2532.2604	5140.0307	0.0000	1.0000
K2P	36	-2533.3210	5142.1518	0.0000	1.0000
SYM	40	-2534.1362	5152.6167	0.0000	1.0000
F81	38	-2574.5068	5228.9291	0.0000	1.0000
JC69	35	-2583.3764	5240.0686	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2461.4686	5010.9372	0.4293	0.4293
HKYG	40	-2465.8510	5011.7019	0.2929	0.7221
HKYI	40	-2466.3514	5012.7027	0.1776	0.8997
HKYIG	41	-2465.9707	5013.9414	0.0956	0.9953
GTRIG	45	-2465.4771	5020.9543	0.0029	0.9982
GTRI	44	-2467.0503	5022.1005	0.0016	0.9998
K2PG	37	-2476.6586	5027.3173	0.0001	0.9999
K2PI	37	-2477.1820	5028.3641	0.0001	1.0000
K2PIG	38	-2476.7688	5029.5376	0.0000	1.0000
SYMG	41	-2479.6414	5041.2827	0.0000	1.0000
SYMIG	42	-2479.3927	5042.7855	0.0000	1.0000
SYMI	41	-2480.7573	5043.5146	0.0000	1.0000
F81G	39	-2520.4967	5118.9935	0.0000	1.0000
HKY	39	-2522.5673	5123.1346	0.0000	1.0000
F81IG	40	-2522.1607	5124.3214	0.0000	1.0000
F81I	39	-2523.5430	5125.0860	0.0000	1.0000
GTR	43	-2520.4994	5126.9989	0.0000	1.0000
JC69G	36	-2528.7808	5129.5616	0.0000	1.0000
JC69IG	37	-2530.9107	5135.8214	0.0000	1.0000
JC69I	36	-2532.2604	5136.5208	0.0000	1.0000
K2P	36	-2533.3210	5138.6419	0.0000	1.0000
SYM	40	-2534.1362	5148.2723	0.0000	1.0000
F81	38	-2574.5068	5225.0137	0.0000	1.0000
JC69	35	-2583.3764	5236.7529	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2465.8510	5198.8859	0.4208	0.4208
HKYI	40	-2466.3514	5199.8867	0.2551	0.6760
K2PG	37	-2476.6586	5200.4624	0.1913	0.8673
K2PI	37	-2477.1820	5201.5092	0.1134	0.9806
HKYIG	41	-2465.9707	5205.8050	0.0132	0.9939
K2PIG	38	-2476.7688	5207.3624	0.0061	0.9999
GTRG	44	-2461.4686	5216.8395	0.0001	1.0000
GTRI	44	-2467.0503	5228.0029	0.0000	1.0000
GTRIG	45	-2465.4771	5231.5362	0.0000	1.0000
SYMG	41	-2479.6414	5233.1463	0.0000	1.0000
SYMI	41	-2480.7573	5235.3782	0.0000	1.0000
SYMIG	42	-2479.3927	5239.3286	0.0000	1.0000
JC69G	36	-2528.7808	5298.0272	0.0000	1.0000
F81G	39	-2520.4967	5301.4978	0.0000	1.0000
JC69I	36	-2532.2604	5304.9864	0.0000	1.0000
HKY	39	-2522.5673	5305.6390	0.0000	1.0000
K2P	36	-2533.3210	5307.1075	0.0000	1.0000
F81I	39	-2523.5430	5307.5904	0.0000	1.0000
JC69IG	37	-2530.9107	5308.9665	0.0000	1.0000
F81IG	40	-2522.1607	5311.5053	0.0000	1.0000
GTR	43	-2520.4994	5328.2217	0.0000	1.0000
SYM	40	-2534.1362	5335.4563	0.0000	1.0000
JC69	35	-2583.3764	5400.5388	0.0000	1.0000
F81	38	-2574.5068	5402.8384	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/chr3_6231.phylip = 1 - 796;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6231.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/chr3_6231.phylip = 1 - 796;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6231.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/chr3_6231.phylip = 1 - 796;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6231.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

