
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:32 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/chr5_11339.phylip" (19 taxa, 746 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	-3066.1860	6226.0210	0.7178	0.7178
GTRIG	45	-3066.1004	6228.1151	0.2519	0.9697
GTRI	44	-3069.7067	6233.0624	0.0212	0.9910
HKYG	40	-3075.3827	6235.4178	0.0065	0.9975
HKYIG	41	-3075.3103	6237.5126	0.0023	0.9998
HKYI	40	-3078.8470	6242.3465	0.0002	1.0000
K2PG	37	-3097.0367	6272.0451	0.0000	1.0000
SYMG	41	-3092.7747	6272.4414	0.0000	1.0000
K2PIG	38	-3096.9725	6274.1373	0.0000	1.0000
SYMIG	42	-3092.7303	6274.5985	0.0000	1.0000
SYMI	41	-3096.1450	6279.1820	0.0000	1.0000
K2PI	37	-3100.7189	6279.4096	0.0000	1.0000
GTR	43	-3117.6758	6326.7418	0.0000	1.0000
HKY	39	-3126.1274	6334.6741	0.0000	1.0000
SYM	40	-3142.6118	6369.8762	0.0000	1.0000
K2P	36	-3147.9934	6371.7442	0.0000	1.0000
F81G	39	-3167.3250	6417.0693	0.0000	1.0000
F81IG	40	-3167.3004	6419.2533	0.0000	1.0000
F81I	39	-3170.5486	6423.5165	0.0000	1.0000
JC69G	36	-3183.2630	6442.2833	0.0000	1.0000
JC69IG	37	-3183.2392	6444.4502	0.0000	1.0000
JC69I	36	-3186.5887	6448.9347	0.0000	1.0000
F81	38	-3215.9723	6512.1370	0.0000	1.0000
JC69	35	-3230.1073	6533.7638	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3066.1860	6220.3720	0.6953	0.6953
GTRIG	45	-3066.1004	6222.2009	0.2786	0.9739
GTRI	44	-3069.7067	6227.4133	0.0206	0.9945
HKYG	40	-3075.3827	6230.7653	0.0038	0.9984
HKYIG	41	-3075.3103	6232.6206	0.0015	0.9999
HKYI	40	-3078.8470	6237.6940	0.0001	1.0000
SYMG	41	-3092.7747	6267.5493	0.0000	1.0000
K2PG	37	-3097.0367	6268.0733	0.0000	1.0000
SYMIG	42	-3092.7303	6269.4605	0.0000	1.0000
K2PIG	38	-3096.9725	6269.9449	0.0000	1.0000
SYMI	41	-3096.1450	6274.2899	0.0000	1.0000
K2PI	37	-3100.7189	6275.4379	0.0000	1.0000
GTR	43	-3117.6758	6321.3515	0.0000	1.0000
HKY	39	-3126.1274	6330.2548	0.0000	1.0000
SYM	40	-3142.6118	6365.2237	0.0000	1.0000
K2P	36	-3147.9934	6367.9868	0.0000	1.0000
F81G	39	-3167.3250	6412.6500	0.0000	1.0000
F81IG	40	-3167.3004	6414.6009	0.0000	1.0000
F81I	39	-3170.5486	6419.0972	0.0000	1.0000
JC69G	36	-3183.2630	6438.5259	0.0000	1.0000
JC69IG	37	-3183.2392	6440.4784	0.0000	1.0000
JC69I	36	-3186.5887	6445.1773	0.0000	1.0000
F81	38	-3215.9723	6507.9446	0.0000	1.0000
JC69	35	-3230.1073	6530.2145	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3075.3827	6415.3544	0.9178	0.9178
HKYIG	41	-3075.3103	6421.8243	0.0361	0.9539
HKYI	40	-3078.8470	6422.2831	0.0287	0.9826
GTRG	44	-3066.1860	6423.4199	0.0163	0.9989
GTRIG	45	-3066.1004	6429.8635	0.0006	0.9995
GTRI	44	-3069.7067	6430.4612	0.0005	1.0000
K2PG	37	-3097.0367	6438.8181	0.0000	1.0000
K2PIG	38	-3096.9725	6445.3045	0.0000	1.0000
K2PI	37	-3100.7189	6446.1827	0.0000	1.0000
SYMG	41	-3092.7747	6456.7531	0.0000	1.0000
SYMIG	42	-3092.7303	6463.2790	0.0000	1.0000
SYMI	41	-3096.1450	6463.4937	0.0000	1.0000
HKY	39	-3126.1274	6510.2291	0.0000	1.0000
GTR	43	-3117.6758	6519.7847	0.0000	1.0000
K2P	36	-3147.9934	6534.1169	0.0000	1.0000
SYM	40	-3142.6118	6549.8127	0.0000	1.0000
F81G	39	-3167.3250	6592.6243	0.0000	1.0000
F81I	39	-3170.5486	6599.0715	0.0000	1.0000
F81IG	40	-3167.3004	6599.1899	0.0000	1.0000
JC69G	36	-3183.2630	6604.6560	0.0000	1.0000
JC69IG	37	-3183.2392	6611.2233	0.0000	1.0000
JC69I	36	-3186.5887	6611.3075	0.0000	1.0000
F81	38	-3215.9723	6683.3042	0.0000	1.0000
JC69	35	-3230.1073	6691.7299	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/chr5_11339.phylip = 1 - 746;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11339.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/chr5_11339.phylip = 1 - 746;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11339.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/chr5_11339.phylip = 1 - 746;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11339.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

