
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:52 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/chr5_3415.phylip" (19 taxa, 664 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2774.9244	5644.2462	0.5580	0.5580
GTRIG	45	-2774.2450	5645.1891	0.3483	0.9063
HKYG	40	-2781.5935	5648.4518	0.0681	0.9744
HKYIG	41	-2781.5934	5650.7238	0.0219	0.9963
GTRI	44	-2780.5747	5655.5467	0.0020	0.9983
HKYI	40	-2785.2616	5655.7881	0.0017	1.0000
SYMG	41	-2798.9573	5685.4516	0.0000	1.0000
SYMIG	42	-2798.9589	5687.7343	0.0000	1.0000
SYMI	41	-2804.3475	5696.2319	0.0000	1.0000
K2PG	37	-2808.9936	5696.4793	0.0000	1.0000
K2PIG	38	-2811.5723	5703.8870	0.0000	1.0000
K2PI	37	-2815.1878	5708.8676	0.0000	1.0000
F81IG	40	-2878.4035	5842.0718	0.0000	1.0000
F81I	39	-2881.2045	5845.4090	0.0000	1.0000
F81G	39	-2885.7819	5854.5637	0.0000	1.0000
GTR	43	-2881.7475	5855.5982	0.0000	1.0000
HKY	39	-2888.6553	5860.3106	0.0000	1.0000
JC69IG	37	-2898.6752	5875.8424	0.0000	1.0000
JC69I	36	-2900.2823	5876.8135	0.0000	1.0000
JC69G	36	-2905.2240	5886.6969	0.0000	1.0000
SYM	40	-2904.7411	5894.7470	0.0000	1.0000
K2P	36	-2916.5957	5909.4403	0.0000	1.0000
F81	38	-2977.4919	6035.7262	0.0000	1.0000
JC69	35	-2995.9024	6065.8175	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2774.9244	5637.8488	0.5477	0.5477
GTRIG	45	-2774.2450	5638.4900	0.3975	0.9452
HKYG	40	-2781.5935	5643.1870	0.0380	0.9831
HKYIG	41	-2781.5934	5645.1868	0.0140	0.9971
GTRI	44	-2780.5747	5649.1493	0.0019	0.9990
HKYI	40	-2785.2616	5650.5233	0.0010	1.0000
SYMG	41	-2798.9573	5679.9146	0.0000	1.0000
SYMIG	42	-2798.9589	5681.9179	0.0000	1.0000
SYMI	41	-2804.3475	5690.6949	0.0000	1.0000
K2PG	37	-2808.9936	5691.9873	0.0000	1.0000
K2PIG	38	-2811.5723	5699.1446	0.0000	1.0000
K2PI	37	-2815.1878	5704.3755	0.0000	1.0000
F81IG	40	-2878.4035	5836.8070	0.0000	1.0000
F81I	39	-2881.2045	5840.4090	0.0000	1.0000
GTR	43	-2881.7475	5849.4950	0.0000	1.0000
F81G	39	-2885.7819	5849.5637	0.0000	1.0000
HKY	39	-2888.6553	5855.3106	0.0000	1.0000
JC69IG	37	-2898.6752	5871.3504	0.0000	1.0000
JC69I	36	-2900.2823	5872.5647	0.0000	1.0000
JC69G	36	-2905.2240	5882.4481	0.0000	1.0000
SYM	40	-2904.7411	5889.4821	0.0000	1.0000
K2P	36	-2916.5957	5905.1915	0.0000	1.0000
F81	38	-2977.4919	6030.9838	0.0000	1.0000
JC69	35	-2995.9024	6061.8048	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2781.5935	5823.1183	0.9379	0.9379
HKYIG	41	-2781.5934	5829.6164	0.0364	0.9743
HKYI	40	-2785.2616	5830.4545	0.0239	0.9982
GTRG	44	-2774.9244	5835.7732	0.0017	0.9999
GTRIG	45	-2774.2450	5840.9127	0.0001	1.0000
GTRI	44	-2780.5747	5847.0737	0.0000	1.0000
K2PG	37	-2808.9936	5858.4237	0.0000	1.0000
SYMG	41	-2798.9573	5864.3442	0.0000	1.0000
K2PIG	38	-2811.5723	5870.0794	0.0000	1.0000
K2PI	37	-2815.1878	5870.8120	0.0000	1.0000
SYMIG	42	-2798.9589	5870.8457	0.0000	1.0000
SYMI	41	-2804.3475	5875.1245	0.0000	1.0000
F81I	39	-2881.2045	6015.8420	0.0000	1.0000
F81IG	40	-2878.4035	6016.7382	0.0000	1.0000
F81G	39	-2885.7819	6024.9967	0.0000	1.0000
HKY	39	-2888.6553	6030.7436	0.0000	1.0000
JC69I	36	-2900.2823	6034.5028	0.0000	1.0000
JC69IG	37	-2898.6752	6037.7868	0.0000	1.0000
GTR	43	-2881.7475	6042.9211	0.0000	1.0000
JC69G	36	-2905.2240	6044.3863	0.0000	1.0000
K2P	36	-2916.5957	6067.1297	0.0000	1.0000
SYM	40	-2904.7411	6069.4134	0.0000	1.0000
F81	38	-2977.4919	6201.9185	0.0000	1.0000
JC69	35	-2995.9024	6219.2446	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/chr5_3415.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3415.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3415.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3415.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3415.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3415.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

