
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:52 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/chr7_10687.phylip" (19 taxa, 790 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	-3026.3555	6146.0264	0.5027	0.5027
GTRIG	45	-3026.0419	6147.6483	0.2234	0.7262
HKYG	40	-3031.7879	6147.9551	0.1917	0.9178
HKYIG	41	-3031.5228	6149.6498	0.0821	1.0000
GTRI	44	-3036.2145	6165.7445	0.0000	1.0000
HKYI	40	-3041.2606	6166.9004	0.0000	1.0000
K2PG	37	-3054.2423	6186.2239	0.0000	1.0000
K2PIG	38	-3053.9683	6187.8834	0.0000	1.0000
SYMG	41	-3053.2620	6193.1283	0.0000	1.0000
SYMIG	42	-3052.9762	6194.7877	0.0000	1.0000
K2PI	37	-3062.9568	6203.6529	0.0000	1.0000
SYMI	41	-3062.0626	6210.7296	0.0000	1.0000
GTR	43	-3079.7611	6250.5946	0.0000	1.0000
HKY	39	-3084.3009	6250.7618	0.0000	1.0000
K2P	36	-3107.0186	6289.5751	0.0000	1.0000
F81G	39	-3104.8631	6291.8862	0.0000	1.0000
F81IG	40	-3104.6713	6293.7219	0.0000	1.0000
SYM	40	-3106.1424	6296.6640	0.0000	1.0000
F81I	39	-3113.1021	6308.3642	0.0000	1.0000
JC69G	36	-3124.0354	6323.6086	0.0000	1.0000
JC69IG	37	-3123.8785	6325.4963	0.0000	1.0000
JC69I	36	-3131.9492	6339.4362	0.0000	1.0000
F81	38	-3154.7306	6389.4079	0.0000	1.0000
JC69	35	-3174.4853	6422.3127	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3026.3555	6140.7110	0.5386	0.5386
GTRIG	45	-3026.0419	6142.0838	0.2711	0.8097
HKYG	40	-3031.7879	6143.5759	0.1286	0.9383
HKYIG	41	-3031.5228	6145.0455	0.0617	1.0000
GTRI	44	-3036.2145	6160.4290	0.0000	1.0000
HKYI	40	-3041.2606	6162.5212	0.0000	1.0000
K2PG	37	-3054.2423	6182.4846	0.0000	1.0000
K2PIG	38	-3053.9683	6183.9366	0.0000	1.0000
SYMG	41	-3053.2620	6188.5240	0.0000	1.0000
SYMIG	42	-3052.9762	6189.9523	0.0000	1.0000
K2PI	37	-3062.9568	6199.9135	0.0000	1.0000
SYMI	41	-3062.0626	6206.1253	0.0000	1.0000
GTR	43	-3079.7611	6245.5222	0.0000	1.0000
HKY	39	-3084.3009	6246.6018	0.0000	1.0000
K2P	36	-3107.0186	6286.0373	0.0000	1.0000
F81G	39	-3104.8631	6287.7262	0.0000	1.0000
F81IG	40	-3104.6713	6289.3427	0.0000	1.0000
SYM	40	-3106.1424	6292.2849	0.0000	1.0000
F81I	39	-3113.1021	6304.2042	0.0000	1.0000
JC69G	36	-3124.0354	6320.0707	0.0000	1.0000
JC69IG	37	-3123.8785	6321.7569	0.0000	1.0000
JC69I	36	-3131.9492	6335.8983	0.0000	1.0000
F81	38	-3154.7306	6385.4612	0.0000	1.0000
JC69	35	-3174.4853	6418.9705	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3031.7879	6330.4572	0.9552	0.9552
HKYIG	41	-3031.5228	6336.5989	0.0443	0.9996
GTRG	44	-3026.3555	6346.2804	0.0004	0.9999
HKYI	40	-3041.2606	6349.4025	0.0001	1.0000
GTRIG	45	-3026.0419	6352.3253	0.0000	1.0000
K2PG	37	-3054.2423	6355.3498	0.0000	1.0000
K2PIG	38	-3053.9683	6361.4739	0.0000	1.0000
GTRI	44	-3036.2145	6365.9985	0.0000	1.0000
K2PI	37	-3062.9568	6372.7788	0.0000	1.0000
SYMG	41	-3053.2620	6380.0773	0.0000	1.0000
SYMIG	42	-3052.9762	6386.1777	0.0000	1.0000
SYMI	41	-3062.0626	6397.6787	0.0000	1.0000
HKY	39	-3084.3009	6428.8111	0.0000	1.0000
GTR	43	-3079.7611	6446.4196	0.0000	1.0000
K2P	36	-3107.0186	6454.2304	0.0000	1.0000
F81G	39	-3104.8631	6469.9355	0.0000	1.0000
F81IG	40	-3104.6713	6476.2240	0.0000	1.0000
SYM	40	-3106.1424	6479.1662	0.0000	1.0000
F81I	39	-3113.1021	6486.4135	0.0000	1.0000
JC69G	36	-3124.0354	6488.2639	0.0000	1.0000
JC69IG	37	-3123.8785	6494.6221	0.0000	1.0000
JC69I	36	-3131.9492	6504.0915	0.0000	1.0000
F81	38	-3154.7306	6562.9984	0.0000	1.0000
JC69	35	-3174.4853	6582.4917	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/chr7_10687.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10687.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/chr7_10687.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10687.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/chr7_10687.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10687.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

