
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:42 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/chr26_2177.phylip" (19 taxa, 673 characters)

Minimum AIC  model: GTRIG
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	-2794.9217	5684.1491	0.3618	0.3618
GTRIG	45	-2793.8408	5684.2845	0.3381	0.6999
GTRI	44	-2795.2665	5684.8387	0.2563	0.9561
HKYG	40	-2802.1011	5689.3922	0.0263	0.9824
HKYIG	41	-2801.7229	5690.9037	0.0124	0.9948
HKYI	40	-2803.7183	5692.6265	0.0052	1.0000
SYMG	41	-2820.8596	5729.1773	0.0000	1.0000
SYMI	41	-2822.0843	5731.6265	0.0000	1.0000
SYMIG	42	-2821.3046	5732.3425	0.0000	1.0000
K2PG	37	-2827.3506	5733.1295	0.0000	1.0000
K2PI	37	-2828.4939	5735.4161	0.0000	1.0000
K2PIG	38	-2827.6923	5736.0596	0.0000	1.0000
GTR	43	-2843.7297	5779.4754	0.0000	1.0000
HKY	39	-2857.9601	5798.8490	0.0000	1.0000
F81G	39	-2868.8071	5820.5431	0.0000	1.0000
F81I	39	-2869.1615	5821.2519	0.0000	1.0000
F81IG	40	-2868.2949	5821.7797	0.0000	1.0000
SYM	40	-2871.1399	5827.4697	0.0000	1.0000
K2P	36	-2882.2221	5840.6329	0.0000	1.0000
JC69G	36	-2896.4603	5869.1093	0.0000	1.0000
JC69I	36	-2896.9627	5870.1142	0.0000	1.0000
JC69IG	37	-2895.9913	5870.4109	0.0000	1.0000
F81	38	-2921.6680	5924.0110	0.0000	1.0000
JC69	35	-2944.7598	5963.4756	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2793.8408	5677.6816	0.3785	0.3785
GTRG	44	-2794.9217	5677.8434	0.3491	0.7275
GTRI	44	-2795.2665	5678.5329	0.2473	0.9748
HKYG	40	-2802.1011	5684.2023	0.0145	0.9893
HKYIG	41	-2801.7229	5685.4457	0.0078	0.9971
HKYI	40	-2803.7183	5687.4366	0.0029	1.0000
SYMG	41	-2820.8596	5723.7193	0.0000	1.0000
SYMI	41	-2822.0843	5726.1685	0.0000	1.0000
SYMIG	42	-2821.3046	5726.6091	0.0000	1.0000
K2PG	37	-2827.3506	5728.7011	0.0000	1.0000
K2PI	37	-2828.4939	5730.9878	0.0000	1.0000
K2PIG	38	-2827.6923	5731.3845	0.0000	1.0000
GTR	43	-2843.7297	5773.4595	0.0000	1.0000
HKY	39	-2857.9601	5793.9201	0.0000	1.0000
F81G	39	-2868.8071	5815.6142	0.0000	1.0000
F81I	39	-2869.1615	5816.3230	0.0000	1.0000
F81IG	40	-2868.2949	5816.5898	0.0000	1.0000
SYM	40	-2871.1399	5822.2798	0.0000	1.0000
K2P	36	-2882.2221	5836.4442	0.0000	1.0000
JC69G	36	-2896.4603	5864.9206	0.0000	1.0000
JC69I	36	-2896.9627	5865.9255	0.0000	1.0000
JC69IG	37	-2895.9913	5865.9826	0.0000	1.0000
F81	38	-2921.6680	5919.3359	0.0000	1.0000
JC69	35	-2944.7598	5959.5196	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2802.1011	5864.6721	0.7936	0.7936
HKYI	40	-2803.7183	5867.9065	0.1575	0.9512
HKYIG	41	-2801.7229	5870.4273	0.0447	0.9958
GTRG	44	-2794.9217	5876.3602	0.0023	0.9981
GTRI	44	-2795.2665	5877.0497	0.0016	0.9997
GTRIG	45	-2793.8408	5880.7101	0.0003	1.0000
K2PG	37	-2827.3506	5895.6357	0.0000	1.0000
K2PI	37	-2828.4939	5897.9224	0.0000	1.0000
K2PIG	38	-2827.6923	5902.8308	0.0000	1.0000
SYMG	41	-2820.8596	5908.7008	0.0000	1.0000
SYMI	41	-2822.0843	5911.1501	0.0000	1.0000
SYMIG	42	-2821.3046	5916.1024	0.0000	1.0000
GTR	43	-2843.7297	5967.4645	0.0000	1.0000
HKY	39	-2857.9601	5969.8782	0.0000	1.0000
F81G	39	-2868.8071	5991.5723	0.0000	1.0000
F81I	39	-2869.1615	5992.2810	0.0000	1.0000
F81IG	40	-2868.2949	5997.0596	0.0000	1.0000
K2P	36	-2882.2221	5998.8671	0.0000	1.0000
SYM	40	-2871.1399	6002.7496	0.0000	1.0000
JC69G	36	-2896.4603	6027.3434	0.0000	1.0000
JC69I	36	-2896.9627	6028.3483	0.0000	1.0000
JC69IG	37	-2895.9913	6032.9172	0.0000	1.0000
F81	38	-2921.6680	6090.7823	0.0000	1.0000
JC69	35	-2944.7598	6117.4306	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr26_2177.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr26_2177.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr26_2177.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr26_2177.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/chr26_2177.phylip = 1 - 673;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr26_2177.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

