
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:48 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/chr3_2614.phylip" (19 taxa, 950 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	-3125.4277	6343.2310	0.5052	0.5052
GTRIG	45	-3125.0545	6344.6887	0.2437	0.7489
HKYG	40	-3130.5718	6344.7520	0.2361	0.9850
GTRI	44	-3129.1076	6350.5909	0.0127	0.9978
HKYIG	41	-3134.2891	6354.3711	0.0019	0.9997
HKYI	40	-3137.2747	6358.1578	0.0003	1.0000
SYMG	41	-3175.5396	6436.8722	0.0000	1.0000
K2PG	37	-3181.5115	6440.1063	0.0000	1.0000
K2PIG	38	-3181.3499	6441.9534	0.0000	1.0000
K2PI	37	-3183.5886	6444.2606	0.0000	1.0000
SYMIG	42	-3178.4279	6444.8382	0.0000	1.0000
SYMI	41	-3180.2220	6446.2370	0.0000	1.0000
F81G	39	-3189.4023	6460.2332	0.0000	1.0000
F81IG	40	-3189.2103	6462.0289	0.0000	1.0000
HKY	39	-3190.8676	6463.1638	0.0000	1.0000
F81I	39	-3191.7597	6464.9480	0.0000	1.0000
GTR	43	-3190.6808	6471.5382	0.0000	1.0000
JC69G	36	-3224.0106	6522.9390	0.0000	1.0000
JC69IG	37	-3229.0466	6535.1765	0.0000	1.0000
JC69I	36	-3231.0123	6536.9425	0.0000	1.0000
SYM	40	-3238.0830	6559.7744	0.0000	1.0000
K2P	36	-3247.4546	6569.8271	0.0000	1.0000
F81	38	-3250.7152	6580.6839	0.0000	1.0000
JC69	35	-3282.9354	6638.6280	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3125.4277	6338.8553	0.5316	0.5316
GTRIG	45	-3125.0545	6340.1090	0.2840	0.8156
HKYG	40	-3130.5718	6341.1437	0.1693	0.9849
GTRI	44	-3129.1076	6346.2152	0.0134	0.9983
HKYIG	41	-3134.2891	6350.5781	0.0015	0.9998
HKYI	40	-3137.2747	6354.5494	0.0002	1.0000
SYMG	41	-3175.5396	6433.0792	0.0000	1.0000
K2PG	37	-3181.5115	6437.0229	0.0000	1.0000
K2PIG	38	-3181.3499	6438.6999	0.0000	1.0000
SYMIG	42	-3178.4279	6440.8558	0.0000	1.0000
K2PI	37	-3183.5886	6441.1772	0.0000	1.0000
SYMI	41	-3180.2220	6442.4440	0.0000	1.0000
F81G	39	-3189.4023	6456.8046	0.0000	1.0000
F81IG	40	-3189.2103	6458.4206	0.0000	1.0000
HKY	39	-3190.8676	6459.7352	0.0000	1.0000
F81I	39	-3191.7597	6461.5195	0.0000	1.0000
GTR	43	-3190.6808	6467.3616	0.0000	1.0000
JC69G	36	-3224.0106	6520.0212	0.0000	1.0000
JC69IG	37	-3229.0466	6532.0931	0.0000	1.0000
JC69I	36	-3231.0123	6534.0246	0.0000	1.0000
SYM	40	-3238.0830	6556.1661	0.0000	1.0000
K2P	36	-3247.4546	6566.9093	0.0000	1.0000
F81	38	-3250.7152	6577.4304	0.0000	1.0000
JC69	35	-3282.9354	6635.8708	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3130.5718	6535.4022	0.9978	0.9978
HKYI	40	-3137.2747	6548.8079	0.0012	0.9990
HKYIG	41	-3134.2891	6549.6931	0.0008	0.9998
GTRG	44	-3125.4277	6552.5397	0.0002	1.0000
GTRIG	45	-3125.0545	6558.6498	0.0000	1.0000
GTRI	44	-3129.1076	6559.8995	0.0000	1.0000
K2PG	37	-3181.5115	6616.7120	0.0000	1.0000
K2PI	37	-3183.5886	6620.8663	0.0000	1.0000
K2PIG	38	-3181.3499	6623.2454	0.0000	1.0000
SYMG	41	-3175.5396	6632.1941	0.0000	1.0000
SYMI	41	-3180.2220	6641.5590	0.0000	1.0000
SYMIG	42	-3178.4279	6644.8272	0.0000	1.0000
F81G	39	-3189.4023	6646.2066	0.0000	1.0000
HKY	39	-3190.8676	6649.1372	0.0000	1.0000
F81I	39	-3191.7597	6650.9215	0.0000	1.0000
F81IG	40	-3189.2103	6652.6791	0.0000	1.0000
GTR	43	-3190.6808	6676.1895	0.0000	1.0000
JC69G	36	-3224.0106	6694.8538	0.0000	1.0000
JC69I	36	-3231.0123	6708.8573	0.0000	1.0000
JC69IG	37	-3229.0466	6711.7822	0.0000	1.0000
K2P	36	-3247.4546	6741.7419	0.0000	1.0000
SYM	40	-3238.0830	6750.4246	0.0000	1.0000
F81	38	-3250.7152	6761.9759	0.0000	1.0000
JC69	35	-3282.9354	6805.8470	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/chr3_2614.phylip = 1 - 950;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2614.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/chr3_2614.phylip = 1 - 950;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2614.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/chr3_2614.phylip = 1 - 950;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2614.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

