
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:06 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/chr2_8573.phylip" (19 taxa, 456 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	-1275.2266	2648.0883	0.4598	0.4598
GTRI	44	-1275.3813	2648.3976	0.3939	0.8536
GTRIG	45	-1275.2493	2650.5961	0.1312	0.9848
HKYG	40	-1283.5307	2654.9651	0.0148	0.9996
HKYI	40	-1287.3651	2662.6339	0.0003	0.9999
HKYIG	41	-1287.4938	2665.3063	0.0001	1.0000
SYMG	41	-1300.0972	2690.5132	0.0000	1.0000
SYMI	41	-1300.3411	2691.0010	0.0000	1.0000
SYMIG	42	-1300.0593	2692.8644	0.0000	1.0000
GTR	43	-1300.3011	2695.7866	0.0000	1.0000
K2PG	37	-1309.1699	2699.0671	0.0000	1.0000
F81I	39	-1306.9892	2699.4784	0.0000	1.0000
F81G	39	-1307.1223	2699.7446	0.0000	1.0000
F81IG	40	-1307.1222	2702.1479	0.0000	1.0000
K2PI	37	-1313.2149	2707.1571	0.0000	1.0000
HKY	39	-1310.9375	2707.3750	0.0000	1.0000
K2PIG	38	-1313.3117	2709.7313	0.0000	1.0000
JC69I	36	-1329.6032	2737.5645	0.0000	1.0000
JC69G	36	-1329.7011	2737.7603	0.0000	1.0000
SYM	40	-1324.9509	2737.8053	0.0000	1.0000
JC69IG	37	-1329.7010	2740.1293	0.0000	1.0000
F81	38	-1330.6754	2744.4586	0.0000	1.0000
K2P	36	-1336.5016	2751.3613	0.0000	1.0000
JC69	35	-1353.1065	2782.2130	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1275.2266	2638.4533	0.4484	0.4484
GTRI	44	-1275.3813	2638.7626	0.3841	0.8325
GTRIG	45	-1275.2493	2640.4985	0.1613	0.9938
HKYG	40	-1283.5307	2647.0615	0.0061	0.9998
HKYI	40	-1287.3651	2654.7302	0.0001	1.0000
HKYIG	41	-1287.4938	2656.9875	0.0000	1.0000
SYMG	41	-1300.0972	2682.1944	0.0000	1.0000
SYMI	41	-1300.3411	2682.6822	0.0000	1.0000
SYMIG	42	-1300.0593	2684.1187	0.0000	1.0000
GTR	43	-1300.3011	2686.6021	0.0000	1.0000
F81I	39	-1306.9892	2691.9784	0.0000	1.0000
F81G	39	-1307.1223	2692.2446	0.0000	1.0000
K2PG	37	-1309.1699	2692.3398	0.0000	1.0000
F81IG	40	-1307.1222	2694.2443	0.0000	1.0000
HKY	39	-1310.9375	2699.8750	0.0000	1.0000
K2PI	37	-1313.2149	2700.4298	0.0000	1.0000
K2PIG	38	-1313.3117	2702.6234	0.0000	1.0000
SYM	40	-1324.9509	2729.9017	0.0000	1.0000
JC69I	36	-1329.6032	2731.2065	0.0000	1.0000
JC69G	36	-1329.7011	2731.4023	0.0000	1.0000
JC69IG	37	-1329.7010	2733.4020	0.0000	1.0000
F81	38	-1330.6754	2737.3507	0.0000	1.0000
K2P	36	-1336.5016	2745.0033	0.0000	1.0000
JC69	35	-1353.1065	2776.2130	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1283.5307	2811.9612	0.9439	0.9439
HKYI	40	-1287.3651	2819.6300	0.0204	0.9643
GTRG	44	-1275.2266	2819.8430	0.0183	0.9826
GTRI	44	-1275.3813	2820.1523	0.0157	0.9983
HKYIG	41	-1287.4938	2826.0097	0.0008	0.9992
GTRIG	45	-1275.2493	2826.0107	0.0008	1.0000
K2PG	37	-1309.1699	2844.8721	0.0000	1.0000
SYMG	41	-1300.0972	2851.2166	0.0000	1.0000
SYMI	41	-1300.3411	2851.7044	0.0000	1.0000
F81I	39	-1306.9892	2852.7557	0.0000	1.0000
K2PI	37	-1313.2149	2852.9620	0.0000	1.0000
F81G	39	-1307.1223	2853.0219	0.0000	1.0000
SYMIG	42	-1300.0593	2857.2634	0.0000	1.0000
F81IG	40	-1307.1222	2859.1440	0.0000	1.0000
K2PIG	38	-1313.3117	2859.2781	0.0000	1.0000
HKY	39	-1310.9375	2860.6522	0.0000	1.0000
GTR	43	-1300.3011	2863.8693	0.0000	1.0000
JC69I	36	-1329.6032	2879.6162	0.0000	1.0000
JC69G	36	-1329.7011	2879.8120	0.0000	1.0000
JC69IG	37	-1329.7010	2885.9343	0.0000	1.0000
K2P	36	-1336.5016	2893.4130	0.0000	1.0000
F81	38	-1330.6754	2894.0054	0.0000	1.0000
SYM	40	-1324.9509	2894.8014	0.0000	1.0000
JC69	35	-1353.1065	2920.5003	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/chr2_8573.phylip = 1 - 456;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8573.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/chr2_8573.phylip = 1 - 456;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8573.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/chr2_8573.phylip = 1 - 456;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8573.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

