
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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_5279.phylip" (19 taxa, 859 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	-2693.6910	5480.2470	0.5427	0.5427
GTRIG	45	-2693.3352	5481.7626	0.2544	0.7971
GTRI	44	-2694.6958	5482.2565	0.1987	0.9958
HKYG	40	-2703.5882	5491.1863	0.0023	0.9981
HKYIG	41	-2703.2538	5492.7230	0.0011	0.9991
HKYI	40	-2704.5701	5493.1500	0.0009	1.0000
GTR	43	-2725.6334	5541.9097	0.0000	1.0000
HKY	39	-2734.1791	5550.1678	0.0000	1.0000
K2PG	37	-2758.9103	5595.2457	0.0000	1.0000
K2PI	37	-2759.4354	5596.2959	0.0000	1.0000
K2PIG	38	-2758.4084	5596.4315	0.0000	1.0000
SYMG	41	-2756.9442	5600.1038	0.0000	1.0000
SYMI	41	-2757.5190	5601.2534	0.0000	1.0000
SYMIG	42	-2756.4954	5601.4173	0.0000	1.0000
F81G	39	-2770.8918	5623.5931	0.0000	1.0000
F81I	39	-2771.0568	5623.9231	0.0000	1.0000
F81IG	40	-2770.4005	5624.8107	0.0000	1.0000
K2P	36	-2790.4709	5656.1827	0.0000	1.0000
SYM	40	-2787.9285	5659.8668	0.0000	1.0000
F81	38	-2796.8575	5673.3297	0.0000	1.0000
JC69G	36	-2817.8783	5710.9974	0.0000	1.0000
JC69I	36	-2818.0900	5711.4209	0.0000	1.0000
JC69IG	37	-2817.4210	5712.2671	0.0000	1.0000
JC69	35	-2844.6293	5762.3205	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2693.6910	5475.3821	0.5273	0.5273
GTRIG	45	-2693.3352	5476.6704	0.2769	0.8042
GTRI	44	-2694.6958	5477.3916	0.1931	0.9973
HKYG	40	-2703.5882	5487.1765	0.0014	0.9987
HKYIG	41	-2703.2538	5488.5076	0.0007	0.9995
HKYI	40	-2704.5701	5489.1402	0.0005	1.0000
GTR	43	-2725.6334	5537.2668	0.0000	1.0000
HKY	39	-2734.1791	5546.3583	0.0000	1.0000
K2PG	37	-2758.9103	5591.8206	0.0000	1.0000
K2PIG	38	-2758.4084	5592.8169	0.0000	1.0000
K2PI	37	-2759.4354	5592.8708	0.0000	1.0000
SYMG	41	-2756.9442	5595.8884	0.0000	1.0000
SYMIG	42	-2756.4954	5596.9908	0.0000	1.0000
SYMI	41	-2757.5190	5597.0380	0.0000	1.0000
F81G	39	-2770.8918	5619.7836	0.0000	1.0000
F81I	39	-2771.0568	5620.1135	0.0000	1.0000
F81IG	40	-2770.4005	5620.8009	0.0000	1.0000
K2P	36	-2790.4709	5652.9418	0.0000	1.0000
SYM	40	-2787.9285	5655.8570	0.0000	1.0000
F81	38	-2796.8575	5669.7151	0.0000	1.0000
JC69G	36	-2817.8783	5707.7565	0.0000	1.0000
JC69I	36	-2818.0900	5708.1800	0.0000	1.0000
JC69IG	37	-2817.4210	5708.8420	0.0000	1.0000
JC69	35	-2844.6293	5759.2586	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2703.5882	5677.4073	0.6847	0.6847
HKYI	40	-2704.5701	5679.3710	0.2565	0.9413
HKYIG	41	-2703.2538	5683.4941	0.0326	0.9739
GTRG	44	-2693.6910	5684.6359	0.0184	0.9923
GTRI	44	-2694.6958	5686.6455	0.0068	0.9991
GTRIG	45	-2693.3352	5690.6800	0.0009	1.0000
HKY	39	-2734.1791	5731.8332	0.0000	1.0000
GTR	43	-2725.6334	5741.7649	0.0000	1.0000
K2PG	37	-2758.9103	5767.7841	0.0000	1.0000
K2PI	37	-2759.4354	5768.8343	0.0000	1.0000
K2PIG	38	-2758.4084	5773.5361	0.0000	1.0000
SYMG	41	-2756.9442	5790.8749	0.0000	1.0000
SYMI	41	-2757.5190	5792.0245	0.0000	1.0000
SYMIG	42	-2756.4954	5796.7331	0.0000	1.0000
F81G	39	-2770.8918	5805.2586	0.0000	1.0000
F81I	39	-2771.0568	5805.5885	0.0000	1.0000
F81IG	40	-2770.4005	5811.0317	0.0000	1.0000
K2P	36	-2790.4709	5824.1495	0.0000	1.0000
SYM	40	-2787.9285	5846.0878	0.0000	1.0000
F81	38	-2796.8575	5850.4343	0.0000	1.0000
JC69G	36	-2817.8783	5878.9642	0.0000	1.0000
JC69I	36	-2818.0900	5879.3877	0.0000	1.0000
JC69IG	37	-2817.4210	5884.8054	0.0000	1.0000
JC69	35	-2844.6293	5925.7105	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_5279.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5279.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_5279.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5279.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_5279.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5279.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

