
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:23 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/chr9_1152.phylip" (19 taxa, 530 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYI


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	-1202.9116	2501.9882	0.3334	0.3334
GTRI	44	-1202.9176	2502.0002	0.3314	0.6647
HKYI	40	-1208.8101	2504.3277	0.1035	0.7682
GTRIG	45	-1202.9114	2504.3766	0.1010	0.8692
HKYG	40	-1208.8451	2504.3978	0.0999	0.9691
HKYIG	41	-1208.8449	2506.7471	0.0309	1.0000
GTR	43	-1215.9162	2525.6185	0.0000	1.0000
HKY	39	-1221.2264	2526.8202	0.0000	1.0000
F81I	39	-1227.8545	2540.0763	0.0000	1.0000
F81G	39	-1227.9409	2540.2491	0.0000	1.0000
F81IG	40	-1227.9407	2542.5889	0.0000	1.0000
K2PI	37	-1235.3184	2550.3523	0.0000	1.0000
K2PG	37	-1235.3781	2550.4716	0.0000	1.0000
K2PIG	38	-1235.3779	2552.7924	0.0000	1.0000
SYMI	41	-1232.8617	2554.7808	0.0000	1.0000
SYMG	41	-1232.9126	2554.8826	0.0000	1.0000
SYMIG	42	-1232.9124	2557.2416	0.0000	1.0000
F81	38	-1239.8086	2561.6538	0.0000	1.0000
K2P	36	-1248.0033	2573.4102	0.0000	1.0000
SYM	40	-1245.6614	2578.0304	0.0000	1.0000
JC69I	36	-1252.3207	2582.0451	0.0000	1.0000
JC69G	36	-1252.4109	2582.2255	0.0000	1.0000
JC69IG	37	-1252.4107	2584.5368	0.0000	1.0000
JC69	35	-1264.5542	2604.2096	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1202.9116	2493.8233	0.3690	0.3690
GTRI	44	-1202.9176	2493.8352	0.3668	0.7359
GTRIG	45	-1202.9114	2495.8229	0.1358	0.8717
HKYI	40	-1208.8101	2497.6201	0.0553	0.9270
HKYG	40	-1208.8451	2497.6902	0.0534	0.9804
HKYIG	41	-1208.8449	2499.6898	0.0196	1.0000
GTR	43	-1215.9162	2517.8325	0.0000	1.0000
HKY	39	-1221.2264	2520.4528	0.0000	1.0000
F81I	39	-1227.8545	2533.7090	0.0000	1.0000
F81G	39	-1227.9409	2533.8817	0.0000	1.0000
F81IG	40	-1227.9407	2535.8813	0.0000	1.0000
K2PI	37	-1235.3184	2544.6369	0.0000	1.0000
K2PG	37	-1235.3781	2544.7562	0.0000	1.0000
K2PIG	38	-1235.3779	2546.7557	0.0000	1.0000
SYMI	41	-1232.8617	2547.7234	0.0000	1.0000
SYMG	41	-1232.9126	2547.8252	0.0000	1.0000
SYMIG	42	-1232.9124	2549.8248	0.0000	1.0000
F81	38	-1239.8086	2555.6172	0.0000	1.0000
K2P	36	-1248.0033	2568.0065	0.0000	1.0000
SYM	40	-1245.6614	2571.3228	0.0000	1.0000
JC69I	36	-1252.3207	2576.6415	0.0000	1.0000
JC69G	36	-1252.4109	2576.8218	0.0000	1.0000
JC69IG	37	-1252.4107	2578.8213	0.0000	1.0000
JC69	35	-1264.5542	2599.1083	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1208.8101	2668.5352	0.4975	0.4975
HKYG	40	-1208.8451	2668.6053	0.4803	0.9778
HKYIG	41	-1208.8449	2674.8777	0.0209	0.9986
GTRG	44	-1202.9116	2681.8298	0.0006	0.9993
GTRI	44	-1202.9176	2681.8418	0.0006	0.9999
HKY	39	-1221.2264	2687.0950	0.0000	1.0000
GTRIG	45	-1202.9114	2688.1023	0.0000	1.0000
F81I	39	-1227.8545	2700.3512	0.0000	1.0000
F81G	39	-1227.9409	2700.5239	0.0000	1.0000
GTR	43	-1215.9162	2701.5662	0.0000	1.0000
K2PI	37	-1235.3184	2702.7333	0.0000	1.0000
K2PG	37	-1235.3781	2702.8526	0.0000	1.0000
F81IG	40	-1227.9407	2706.7964	0.0000	1.0000
K2PIG	38	-1235.3779	2709.1250	0.0000	1.0000
F81	38	-1239.8086	2717.9865	0.0000	1.0000
K2P	36	-1248.0033	2721.8301	0.0000	1.0000
SYMI	41	-1232.8617	2722.9114	0.0000	1.0000
SYMG	41	-1232.9126	2723.0132	0.0000	1.0000
SYMIG	42	-1232.9124	2729.2856	0.0000	1.0000
JC69I	36	-1252.3207	2730.4651	0.0000	1.0000
JC69G	36	-1252.4109	2730.6454	0.0000	1.0000
JC69IG	37	-1252.4107	2736.9178	0.0000	1.0000
SYM	40	-1245.6614	2742.2379	0.0000	1.0000
JC69	35	-1264.5542	2748.6590	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/chr9_1152.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1152.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/chr9_1152.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1152.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1152.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_1152.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

