
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:13 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_32310.phylip" (19 taxa, 680 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	-2760.5892	5615.4146	0.7273	0.7273
HKYG	40	-2766.4297	5617.9925	0.2004	0.9277
HKYIG	41	-2766.3854	5620.1688	0.0675	0.9952
GTRIG	45	-2765.0580	5626.6460	0.0026	0.9979
HKYI	40	-2770.9846	5627.1021	0.0021	1.0000
GTRI	44	-2771.7439	5637.7240	0.0000	1.0000
K2PG	37	-2788.7188	5655.8176	0.0000	1.0000
SYMG	41	-2785.8882	5659.1746	0.0000	1.0000
K2PIG	38	-2793.9765	5668.5771	0.0000	1.0000
SYMIG	42	-2791.2138	5672.0979	0.0000	1.0000
K2PI	37	-2799.8816	5678.1433	0.0000	1.0000
SYMI	41	-2796.7269	5680.8519	0.0000	1.0000
GTR	43	-2799.9128	5691.7752	0.0000	1.0000
HKY	39	-2810.9257	5704.7264	0.0000	1.0000
SYM	40	-2823.9358	5733.0045	0.0000	1.0000
K2P	36	-2830.0212	5736.1854	0.0000	1.0000
F81G	39	-2833.1953	5749.2656	0.0000	1.0000
F81IG	40	-2835.7174	5756.5678	0.0000	1.0000
F81I	39	-2841.6654	5766.2058	0.0000	1.0000
JC69G	36	-2849.4520	5775.0470	0.0000	1.0000
JC69IG	37	-2852.6177	5783.6155	0.0000	1.0000
JC69I	36	-2858.3600	5792.8630	0.0000	1.0000
F81	38	-2870.1885	5821.0011	0.0000	1.0000
JC69	35	-2886.2857	5846.4845	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2760.5892	5609.1784	0.8159	0.8159
HKYG	40	-2766.4297	5612.8595	0.1295	0.9454
HKYIG	41	-2766.3854	5614.7707	0.0498	0.9952
GTRIG	45	-2765.0580	5620.1161	0.0034	0.9986
HKYI	40	-2770.9846	5621.9691	0.0014	1.0000
GTRI	44	-2771.7439	5631.4878	0.0000	1.0000
K2PG	37	-2788.7188	5651.4376	0.0000	1.0000
SYMG	41	-2785.8882	5653.7765	0.0000	1.0000
K2PIG	38	-2793.9765	5663.9531	0.0000	1.0000
SYMIG	42	-2791.2138	5666.4276	0.0000	1.0000
K2PI	37	-2799.8816	5673.7632	0.0000	1.0000
SYMI	41	-2796.7269	5675.4538	0.0000	1.0000
GTR	43	-2799.9128	5685.8256	0.0000	1.0000
HKY	39	-2810.9257	5699.8514	0.0000	1.0000
SYM	40	-2823.9358	5727.8715	0.0000	1.0000
K2P	36	-2830.0212	5732.0423	0.0000	1.0000
F81G	39	-2833.1953	5744.3906	0.0000	1.0000
F81IG	40	-2835.7174	5751.4348	0.0000	1.0000
F81I	39	-2841.6654	5761.3308	0.0000	1.0000
JC69G	36	-2849.4520	5770.9039	0.0000	1.0000
JC69IG	37	-2852.6177	5779.2355	0.0000	1.0000
JC69I	36	-2858.3600	5788.7199	0.0000	1.0000
F81	38	-2870.1885	5816.3771	0.0000	1.0000
JC69	35	-2886.2857	5842.5715	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2766.4297	5793.7432	0.9512	0.9512
HKYIG	41	-2766.3854	5800.1765	0.0381	0.9893
HKYI	40	-2770.9846	5802.8528	0.0100	0.9993
GTRG	44	-2760.5892	5808.1505	0.0007	1.0000
K2PG	37	-2788.7188	5818.7550	0.0000	1.0000
GTRIG	45	-2765.0580	5823.6102	0.0000	1.0000
GTRI	44	-2771.7439	5830.4598	0.0000	1.0000
K2PIG	38	-2793.9765	5835.7926	0.0000	1.0000
SYMG	41	-2785.8882	5839.1823	0.0000	1.0000
K2PI	37	-2799.8816	5841.0807	0.0000	1.0000
SYMIG	42	-2791.2138	5856.3555	0.0000	1.0000
SYMI	41	-2796.7269	5860.8596	0.0000	1.0000
HKY	39	-2810.9257	5876.2130	0.0000	1.0000
GTR	43	-2799.9128	5880.2756	0.0000	1.0000
K2P	36	-2830.0212	5894.8376	0.0000	1.0000
SYM	40	-2823.9358	5908.7552	0.0000	1.0000
F81G	39	-2833.1953	5920.7523	0.0000	1.0000
F81IG	40	-2835.7174	5932.3185	0.0000	1.0000
JC69G	36	-2849.4520	5933.6993	0.0000	1.0000
F81I	39	-2841.6654	5937.6924	0.0000	1.0000
JC69IG	37	-2852.6177	5946.5529	0.0000	1.0000
JC69I	36	-2858.3600	5951.5152	0.0000	1.0000
F81	38	-2870.1885	5988.2166	0.0000	1.0000
JC69	35	-2886.2857	6000.8447	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_32310.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32310.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_32310.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32310.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_32310.phylip = 1 - 680;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32310.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

