
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:44 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_14142.phylip" (19 taxa, 499 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1335.1976	2767.1176	0.3849	0.3849
GTRI	44	-1335.6272	2767.9768	0.2505	0.6354
GTRIG	45	-1335.0210	2769.1811	0.1372	0.7726
SYMG	41	-1340.0294	2769.5950	0.1115	0.8841
SYMI	41	-1340.4040	2770.3441	0.0767	0.9608
SYMIG	42	-1339.8961	2771.7133	0.0387	0.9994
K2PG	37	-1351.2752	2782.6503	0.0002	0.9996
K2PI	37	-1351.6753	2783.4504	0.0001	0.9997
HKYG	40	-1348.1528	2783.4671	0.0001	0.9998
HKYI	40	-1348.5508	2784.2632	0.0001	0.9999
K2PIG	38	-1351.1370	2784.7175	0.0001	1.0000
HKYIG	41	-1348.0056	2785.5473	0.0000	1.0000
SYM	40	-1357.2640	2801.6896	0.0000	1.0000
GTR	43	-1354.2492	2802.8149	0.0000	1.0000
K2P	36	-1367.5085	2812.7832	0.0000	1.0000
HKY	39	-1364.9109	2814.6193	0.0000	1.0000
JC69G	36	-1380.3386	2838.4435	0.0000	1.0000
JC69I	36	-1380.7364	2839.2390	0.0000	1.0000
JC69IG	37	-1380.2141	2840.5279	0.0000	1.0000
F81G	39	-1378.0304	2840.8583	0.0000	1.0000
F81I	39	-1378.4297	2841.6568	0.0000	1.0000
F81IG	40	-1377.8979	2842.9573	0.0000	1.0000
JC69	35	-1396.1840	2867.8108	0.0000	1.0000
F81	38	-1394.1877	2870.8189	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1335.1976	2758.3952	0.4119	0.4119
GTRI	44	-1335.6272	2759.2543	0.2681	0.6800
GTRIG	45	-1335.0210	2760.0420	0.1808	0.8608
SYMG	41	-1340.0294	2762.0589	0.0660	0.9267
SYMI	41	-1340.4040	2762.8080	0.0453	0.9721
SYMIG	42	-1339.8961	2763.7922	0.0277	0.9998
HKYG	40	-1348.1528	2776.3056	0.0001	0.9998
K2PG	37	-1351.2752	2776.5505	0.0000	0.9999
HKYI	40	-1348.5508	2777.1016	0.0000	0.9999
K2PI	37	-1351.6753	2777.3507	0.0000	1.0000
HKYIG	41	-1348.0056	2778.0112	0.0000	1.0000
K2PIG	38	-1351.1370	2778.2741	0.0000	1.0000
GTR	43	-1354.2492	2794.4984	0.0000	1.0000
SYM	40	-1357.2640	2794.5280	0.0000	1.0000
K2P	36	-1367.5085	2807.0169	0.0000	1.0000
HKY	39	-1364.9109	2807.8219	0.0000	1.0000
JC69G	36	-1380.3386	2832.6773	0.0000	1.0000
JC69I	36	-1380.7364	2833.4727	0.0000	1.0000
F81G	39	-1378.0304	2834.0609	0.0000	1.0000
JC69IG	37	-1380.2141	2834.4282	0.0000	1.0000
F81I	39	-1378.4297	2834.8594	0.0000	1.0000
F81IG	40	-1377.8979	2835.7958	0.0000	1.0000
JC69	35	-1396.1840	2862.3681	0.0000	1.0000
F81	38	-1394.1877	2864.3754	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1351.2752	2932.4169	0.4414	0.4414
K2PI	37	-1351.6753	2933.2171	0.2958	0.7372
SYMG	41	-1340.0294	2934.7757	0.1357	0.8729
SYMI	41	-1340.4040	2935.5249	0.0933	0.9662
K2PIG	38	-1351.1370	2938.3531	0.0227	0.9889
SYMIG	42	-1339.8961	2940.7217	0.0069	0.9958
GTRG	44	-1335.1976	2943.7498	0.0015	0.9974
GTRI	44	-1335.6272	2944.6090	0.0010	0.9984
HKYG	40	-1348.1528	2944.8098	0.0009	0.9993
HKYI	40	-1348.5508	2945.6058	0.0006	0.9999
GTRIG	45	-1335.0210	2949.6093	0.0001	1.0000
HKYIG	41	-1348.0056	2950.7281	0.0000	1.0000
K2P	36	-1367.5085	2958.6707	0.0000	1.0000
SYM	40	-1357.2640	2963.0323	0.0000	1.0000
HKY	39	-1364.9109	2972.1135	0.0000	1.0000
GTR	43	-1354.2492	2975.6405	0.0000	1.0000
JC69G	36	-1380.3386	2984.3311	0.0000	1.0000
JC69I	36	-1380.7364	2985.1265	0.0000	1.0000
JC69IG	37	-1380.2141	2990.2946	0.0000	1.0000
F81G	39	-1378.0304	2998.3525	0.0000	1.0000
F81I	39	-1378.4297	2999.1511	0.0000	1.0000
F81IG	40	-1377.8979	3004.3000	0.0000	1.0000
JC69	35	-1396.1840	3009.8093	0.0000	1.0000
F81	38	-1394.1877	3024.4544	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_14142.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14142.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_14142.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14142.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14142.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_14142.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

