
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:10 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/chrZ_3358.phylip" (19 taxa, 978 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	-3454.0992	7000.4429	0.7500	0.7500
GTRIG	45	-3454.0998	7002.6416	0.2498	0.9999
HKYG	40	-3467.5100	7018.5205	0.0001	1.0000
HKYIG	41	-3467.4722	7020.6239	0.0000	1.0000
GTRI	44	-3466.3514	7024.9471	0.0000	1.0000
HKYI	40	-3478.7971	7041.0947	0.0000	1.0000
K2PG	37	-3498.7357	7074.4628	0.0000	1.0000
SYMG	41	-3495.7867	7077.2528	0.0000	1.0000
K2PIG	38	-3499.3390	7077.8346	0.0000	1.0000
SYMIG	42	-3495.7489	7079.3608	0.0000	1.0000
GTR	43	-3496.4279	7082.9071	0.0000	1.0000
K2PI	37	-3508.0170	7093.0256	0.0000	1.0000
SYMI	41	-3504.3749	7094.4292	0.0000	1.0000
HKY	39	-3511.3759	7104.0780	0.0000	1.0000
SYM	40	-3539.3276	7162.1557	0.0000	1.0000
K2P	36	-3544.8295	7164.4900	0.0000	1.0000
F81G	39	-3549.4297	7180.1856	0.0000	1.0000
F81IG	40	-3549.4208	7182.3421	0.0000	1.0000
F81I	39	-3556.3041	7193.9345	0.0000	1.0000
JC69G	36	-3575.5485	7225.9281	0.0000	1.0000
JC69IG	37	-3575.5342	7228.0600	0.0000	1.0000
JC69I	36	-3582.2191	7239.2692	0.0000	1.0000
F81	38	-3586.5734	7252.3034	0.0000	1.0000
JC69	35	-3613.9857	7300.6466	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3454.0992	6996.1985	0.7311	0.7311
GTRIG	45	-3454.0998	6998.1995	0.2688	0.9999
HKYG	40	-3467.5100	7015.0200	0.0001	1.0000
HKYIG	41	-3467.4722	7016.9444	0.0000	1.0000
GTRI	44	-3466.3514	7020.7027	0.0000	1.0000
HKYI	40	-3478.7971	7037.5941	0.0000	1.0000
K2PG	37	-3498.7357	7071.4713	0.0000	1.0000
SYMG	41	-3495.7867	7073.5734	0.0000	1.0000
K2PIG	38	-3499.3390	7074.6781	0.0000	1.0000
SYMIG	42	-3495.7489	7075.4977	0.0000	1.0000
GTR	43	-3496.4279	7078.8557	0.0000	1.0000
K2PI	37	-3508.0170	7090.0341	0.0000	1.0000
SYMI	41	-3504.3749	7090.7497	0.0000	1.0000
HKY	39	-3511.3759	7100.7518	0.0000	1.0000
SYM	40	-3539.3276	7158.6552	0.0000	1.0000
K2P	36	-3544.8295	7161.6589	0.0000	1.0000
F81G	39	-3549.4297	7176.8594	0.0000	1.0000
F81IG	40	-3549.4208	7178.8415	0.0000	1.0000
F81I	39	-3556.3041	7190.6083	0.0000	1.0000
JC69G	36	-3575.5485	7223.0970	0.0000	1.0000
JC69IG	37	-3575.5342	7225.0685	0.0000	1.0000
JC69I	36	-3582.2191	7236.4382	0.0000	1.0000
F81	38	-3586.5734	7249.1469	0.0000	1.0000
JC69	35	-3613.9857	7297.9714	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3467.5100	7210.4404	0.5704	0.5704
GTRG	44	-3454.0992	7211.1609	0.3979	0.9683
HKYIG	41	-3467.4722	7217.2503	0.0189	0.9873
GTRIG	45	-3454.0998	7218.0475	0.0127	1.0000
HKYI	40	-3478.7971	7233.0145	0.0000	1.0000
GTRI	44	-3466.3514	7235.6651	0.0000	1.0000
K2PG	37	-3498.7357	7252.2352	0.0000	1.0000
K2PIG	38	-3499.3390	7260.3274	0.0000	1.0000
K2PI	37	-3508.0170	7270.7980	0.0000	1.0000
SYMG	41	-3495.7867	7273.8793	0.0000	1.0000
SYMIG	42	-3495.7489	7280.6891	0.0000	1.0000
GTR	43	-3496.4279	7288.9326	0.0000	1.0000
SYMI	41	-3504.3749	7291.0556	0.0000	1.0000
HKY	39	-3511.3759	7291.2867	0.0000	1.0000
K2P	36	-3544.8295	7337.5373	0.0000	1.0000
SYM	40	-3539.3276	7354.0755	0.0000	1.0000
F81G	39	-3549.4297	7367.3943	0.0000	1.0000
F81IG	40	-3549.4208	7374.2619	0.0000	1.0000
F81I	39	-3556.3041	7381.1432	0.0000	1.0000
JC69G	36	-3575.5485	7398.9754	0.0000	1.0000
JC69IG	37	-3575.5342	7405.8323	0.0000	1.0000
JC69I	36	-3582.2191	7412.3165	0.0000	1.0000
F81	38	-3586.5734	7434.7962	0.0000	1.0000
JC69	35	-3613.9857	7468.9643	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/chrZ_3358.phylip = 1 - 978;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3358.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/chrZ_3358.phylip = 1 - 978;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3358.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/chrZ_3358.phylip = 1 - 978;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_3358.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

