
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:36 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/chr6_9532.phylip" (19 taxa, 893 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2854.1426	5800.9549	0.3610	0.3610
GTRIG	45	-2853.6297	5802.1473	0.1989	0.5599
HKYG	40	-2859.5378	5802.9253	0.1348	0.6947
SYMG	41	-2858.5356	5803.1181	0.1224	0.8170
HKYIG	41	-2859.0121	5804.0712	0.0760	0.8930
SYMIG	42	-2857.9660	5804.1815	0.0719	0.9650
GTRI	44	-2856.9995	5806.6688	0.0207	0.9857
HKYI	40	-2862.5499	5808.9495	0.0066	0.9923
SYMI	41	-2861.5579	5809.1627	0.0060	0.9983
K2PG	37	-2867.6834	5812.6557	0.0010	0.9993
K2PIG	38	-2867.1045	5813.6797	0.0006	1.0000
K2PI	37	-2870.8020	5818.8929	0.0000	1.0000
F81G	39	-2906.1236	5893.9049	0.0000	1.0000
F81IG	40	-2905.5634	5894.9766	0.0000	1.0000
F81I	39	-2909.3451	5900.3479	0.0000	1.0000
JC69G	36	-2914.8115	5904.7352	0.0000	1.0000
JC69IG	37	-2914.2516	5905.7921	0.0000	1.0000
JC69I	36	-2917.9927	5911.0976	0.0000	1.0000
GTR	43	-2913.9421	5918.3411	0.0000	1.0000
HKY	39	-2918.6084	5918.8746	0.0000	1.0000
SYM	40	-2919.5491	5922.9479	0.0000	1.0000
K2P	36	-2926.8087	5928.7295	0.0000	1.0000
F81	38	-2962.5274	6004.5256	0.0000	1.0000
JC69	35	-2971.2094	6015.3594	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2854.1426	5796.2851	0.3984	0.3984
GTRIG	45	-2853.6297	5797.2594	0.2447	0.6431
SYMG	41	-2858.5356	5799.0711	0.0989	0.7420
HKYG	40	-2859.5378	5799.0755	0.0987	0.8407
SYMIG	42	-2857.9660	5799.9321	0.0643	0.9050
HKYIG	41	-2859.0121	5800.0242	0.0614	0.9665
GTRI	44	-2856.9995	5801.9990	0.0229	0.9894
HKYI	40	-2862.5499	5805.0997	0.0049	0.9942
SYMI	41	-2861.5579	5805.1157	0.0048	0.9990
K2PG	37	-2867.6834	5809.3668	0.0006	0.9996
K2PIG	38	-2867.1045	5810.2090	0.0004	1.0000
K2PI	37	-2870.8020	5815.6040	0.0000	1.0000
F81G	39	-2906.1236	5890.2472	0.0000	1.0000
F81IG	40	-2905.5634	5891.1269	0.0000	1.0000
F81I	39	-2909.3451	5896.6902	0.0000	1.0000
JC69G	36	-2914.8115	5901.6231	0.0000	1.0000
JC69IG	37	-2914.2516	5902.5032	0.0000	1.0000
JC69I	36	-2917.9927	5907.9854	0.0000	1.0000
GTR	43	-2913.9421	5913.8841	0.0000	1.0000
HKY	39	-2918.6084	5915.2169	0.0000	1.0000
SYM	40	-2919.5491	5919.0981	0.0000	1.0000
K2P	36	-2926.8087	5925.6173	0.0000	1.0000
F81	38	-2962.5274	6001.0549	0.0000	1.0000
JC69	35	-2971.2094	6012.4189	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2867.6834	5986.7665	0.7937	0.7937
HKYG	40	-2859.5378	5990.8590	0.1026	0.8963
K2PIG	38	-2867.1045	5992.4033	0.0474	0.9437
K2PI	37	-2870.8020	5993.0037	0.0351	0.9788
SYMG	41	-2858.5356	5995.6492	0.0094	0.9881
HKYIG	41	-2859.0121	5996.6022	0.0058	0.9939
HKYI	40	-2862.5499	5996.8832	0.0050	0.9990
SYMIG	42	-2857.9660	6001.3047	0.0006	0.9995
SYMI	41	-2861.5579	6001.6937	0.0005	1.0000
GTRG	44	-2854.1426	6007.2469	0.0000	1.0000
GTRI	44	-2856.9995	6012.9608	0.0000	1.0000
GTRIG	45	-2853.6297	6013.0158	0.0000	1.0000
JC69G	36	-2914.8115	6074.2282	0.0000	1.0000
F81G	39	-2906.1236	6077.2361	0.0000	1.0000
JC69IG	37	-2914.2516	6079.9029	0.0000	1.0000
JC69I	36	-2917.9927	6080.5905	0.0000	1.0000
F81IG	40	-2905.5634	6082.9103	0.0000	1.0000
F81I	39	-2909.3451	6083.6791	0.0000	1.0000
K2P	36	-2926.8087	6098.2224	0.0000	1.0000
HKY	39	-2918.6084	6102.2058	0.0000	1.0000
SYM	40	-2919.5491	6110.8816	0.0000	1.0000
GTR	43	-2913.9421	6120.0514	0.0000	1.0000
JC69	35	-2971.2094	6180.2294	0.0000	1.0000
F81	38	-2962.5274	6183.2492	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/chr6_9532.phylip = 1 - 893;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9532.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/chr6_9532.phylip = 1 - 893;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9532.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9532.phylip = 1 - 893;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9532.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


-------------------------------------------------------------
End of Output

