
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:02 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_25682.phylip" (19 taxa, 585 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	-2318.6115	4732.5564	0.6958	0.6958
GTRIG	45	-2318.4191	4734.5192	0.2608	0.9566
GTRI	44	-2321.6698	4738.6730	0.0327	0.9893
HKYG	40	-2327.7810	4741.5914	0.0076	0.9969
HKYIG	41	-2327.6159	4743.5743	0.0028	0.9997
HKYI	40	-2331.0469	4748.1231	0.0003	1.0000
GTR	43	-2347.2683	4787.5310	0.0000	1.0000
SYMG	41	-2349.8809	4788.1043	0.0000	1.0000
SYMIG	42	-2349.7102	4790.0846	0.0000	1.0000
K2PG	37	-2355.9480	4791.0368	0.0000	1.0000
K2PIG	38	-2355.7819	4792.9923	0.0000	1.0000
SYMI	41	-2353.4128	4795.1681	0.0000	1.0000
HKY	39	-2356.7298	4797.1843	0.0000	1.0000
K2PI	37	-2359.8526	4798.8460	0.0000	1.0000
SYM	40	-2380.4454	4846.9203	0.0000	1.0000
K2P	36	-2388.0753	4853.0119	0.0000	1.0000
F81G	39	-2406.6910	4897.1068	0.0000	1.0000
F81IG	40	-2406.6008	4899.2311	0.0000	1.0000
F81I	39	-2409.6446	4903.0140	0.0000	1.0000
JC69G	36	-2429.6630	4936.1873	0.0000	1.0000
JC69IG	37	-2429.5664	4938.2736	0.0000	1.0000
JC69I	36	-2433.0438	4942.9488	0.0000	1.0000
F81	38	-2434.8419	4951.1125	0.0000	1.0000
JC69	35	-2459.0105	4992.6112	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2318.6115	4725.2231	0.6661	0.6661
GTRIG	45	-2318.4191	4726.8383	0.2970	0.9631
GTRI	44	-2321.6698	4731.3397	0.0313	0.9944
HKYG	40	-2327.7810	4735.5620	0.0038	0.9982
HKYIG	41	-2327.6159	4737.2318	0.0016	0.9999
HKYI	40	-2331.0469	4742.0937	0.0001	1.0000
GTR	43	-2347.2683	4780.5365	0.0000	1.0000
SYMG	41	-2349.8809	4781.7618	0.0000	1.0000
SYMIG	42	-2349.7102	4783.4204	0.0000	1.0000
K2PG	37	-2355.9480	4785.8961	0.0000	1.0000
K2PIG	38	-2355.7819	4787.5638	0.0000	1.0000
SYMI	41	-2353.4128	4788.8256	0.0000	1.0000
HKY	39	-2356.7298	4791.4596	0.0000	1.0000
K2PI	37	-2359.8526	4793.7052	0.0000	1.0000
SYM	40	-2380.4454	4840.8909	0.0000	1.0000
K2P	36	-2388.0753	4848.1506	0.0000	1.0000
F81G	39	-2406.6910	4891.3820	0.0000	1.0000
F81IG	40	-2406.6008	4893.2017	0.0000	1.0000
F81I	39	-2409.6446	4897.2892	0.0000	1.0000
JC69G	36	-2429.6630	4931.3260	0.0000	1.0000
JC69IG	37	-2429.5664	4933.1328	0.0000	1.0000
JC69I	36	-2433.0438	4938.0875	0.0000	1.0000
F81	38	-2434.8419	4945.6839	0.0000	1.0000
JC69	35	-2459.0105	4988.0210	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2327.7810	4910.4265	0.8947	0.8947
HKYIG	41	-2327.6159	4916.4678	0.0436	0.9383
HKYI	40	-2331.0469	4916.9582	0.0341	0.9725
GTRG	44	-2318.6115	4917.5740	0.0251	0.9976
GTRIG	45	-2318.4191	4923.5608	0.0013	0.9988
GTRI	44	-2321.6698	4923.6906	0.0012	1.0000
K2PG	37	-2355.9480	4947.6457	0.0000	1.0000
K2PIG	38	-2355.7819	4953.6850	0.0000	1.0000
K2PI	37	-2359.8526	4955.4548	0.0000	1.0000
SYMG	41	-2349.8809	4960.9979	0.0000	1.0000
HKY	39	-2356.7298	4961.9524	0.0000	1.0000
SYMIG	42	-2349.7102	4967.0281	0.0000	1.0000
SYMI	41	-2353.4128	4968.0617	0.0000	1.0000
GTR	43	-2347.2683	4968.5158	0.0000	1.0000
K2P	36	-2388.0753	5005.5286	0.0000	1.0000
SYM	40	-2380.4454	5015.7554	0.0000	1.0000
F81G	39	-2406.6910	5061.8748	0.0000	1.0000
F81I	39	-2409.6446	5067.7821	0.0000	1.0000
F81IG	40	-2406.6008	5068.0661	0.0000	1.0000
JC69G	36	-2429.6630	5088.7040	0.0000	1.0000
JC69IG	37	-2429.5664	5094.8825	0.0000	1.0000
JC69I	36	-2433.0438	5095.4655	0.0000	1.0000
F81	38	-2434.8419	5111.8052	0.0000	1.0000
JC69	35	-2459.0105	5141.0274	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/chr1_25682.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25682.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/chr1_25682.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25682.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/chr1_25682.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25682.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

