
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:27 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/chr17_3035.phylip" (19 taxa, 351 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	-1341.2428	2783.4268	0.4791	0.4791
GTRIG	45	-1341.0929	2785.7595	0.1492	0.6283
GTRI	44	-1342.4419	2785.8251	0.1444	0.7728
HKYG	40	-1347.6237	2785.8281	0.1442	0.9170
HKYIG	41	-1347.4808	2788.1073	0.0461	0.9631
HKYI	40	-1348.9878	2788.5562	0.0369	1.0000
K2PG	37	-1362.6427	2808.2694	0.0000	1.0000
K2PIG	38	-1362.4801	2810.4603	0.0000	1.0000
SYMG	41	-1358.6888	2810.5233	0.0000	1.0000
K2PI	37	-1364.1636	2811.3113	0.0000	1.0000
GTR	43	-1356.9613	2812.2483	0.0000	1.0000
SYMI	41	-1359.7876	2812.7208	0.0000	1.0000
SYMIG	42	-1358.5225	2812.7723	0.0000	1.0000
HKY	39	-1365.8453	2819.7227	0.0000	1.0000
F81G	39	-1369.6315	2827.2952	0.0000	1.0000
F81I	39	-1370.7822	2829.5966	0.0000	1.0000
F81IG	40	-1369.5169	2829.6144	0.0000	1.0000
JC69G	36	-1381.9875	2844.4591	0.0000	1.0000
SYM	40	-1376.9420	2844.4646	0.0000	1.0000
K2P	36	-1382.5707	2845.6256	0.0000	1.0000
JC69IG	37	-1381.8652	2846.7144	0.0000	1.0000
JC69I	36	-1383.2017	2846.8876	0.0000	1.0000
F81	38	-1388.0078	2861.5157	0.0000	1.0000
JC69	35	-1401.4843	2880.9687	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1341.2428	2770.4857	0.5307	0.5307
GTRIG	45	-1341.0929	2772.1857	0.2268	0.7576
GTRI	44	-1342.4419	2772.8839	0.1600	0.9176
HKYG	40	-1347.6237	2775.2474	0.0491	0.9666
HKYIG	41	-1347.4808	2776.9617	0.0208	0.9875
HKYI	40	-1348.9878	2777.9756	0.0125	1.0000
K2PG	37	-1362.6427	2799.2854	0.0000	1.0000
SYMG	41	-1358.6888	2799.3776	0.0000	1.0000
GTR	43	-1356.9613	2799.9226	0.0000	1.0000
K2PIG	38	-1362.4801	2800.9603	0.0000	1.0000
SYMIG	42	-1358.5225	2801.0450	0.0000	1.0000
SYMI	41	-1359.7876	2801.5751	0.0000	1.0000
K2PI	37	-1364.1636	2802.3273	0.0000	1.0000
HKY	39	-1365.8453	2809.6905	0.0000	1.0000
F81G	39	-1369.6315	2817.2631	0.0000	1.0000
F81IG	40	-1369.5169	2819.0337	0.0000	1.0000
F81I	39	-1370.7822	2819.5644	0.0000	1.0000
SYM	40	-1376.9420	2833.8840	0.0000	1.0000
JC69G	36	-1381.9875	2835.9750	0.0000	1.0000
K2P	36	-1382.5707	2837.1415	0.0000	1.0000
JC69IG	37	-1381.8652	2837.7303	0.0000	1.0000
JC69I	36	-1383.2017	2838.4035	0.0000	1.0000
F81	38	-1388.0078	2852.0157	0.0000	1.0000
JC69	35	-1401.4843	2872.9687	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1347.6237	2929.6789	0.7540	0.7540
HKYI	40	-1348.9878	2932.4070	0.1927	0.9467
HKYIG	41	-1347.4808	2935.2539	0.0464	0.9932
GTRG	44	-1341.2428	2940.3603	0.0036	0.9968
K2PG	37	-1362.6427	2942.1345	0.0015	0.9983
GTRI	44	-1342.4419	2942.7585	0.0011	0.9994
K2PI	37	-1364.1636	2945.1764	0.0003	0.9997
GTRIG	45	-1341.0929	2945.9211	0.0002	0.9999
K2PIG	38	-1362.4801	2947.6702	0.0001	1.0000
SYMG	41	-1358.6888	2957.6699	0.0000	1.0000
SYMI	41	-1359.7876	2959.8674	0.0000	1.0000
HKY	39	-1365.8453	2960.2612	0.0000	1.0000
SYMIG	42	-1358.5225	2963.1980	0.0000	1.0000
GTR	43	-1356.9613	2965.9364	0.0000	1.0000
F81G	39	-1369.6315	2967.8337	0.0000	1.0000
F81I	39	-1370.7822	2970.1351	0.0000	1.0000
F81IG	40	-1369.5169	2973.4652	0.0000	1.0000
JC69G	36	-1381.9875	2974.9633	0.0000	1.0000
K2P	36	-1382.5707	2976.1298	0.0000	1.0000
JC69I	36	-1383.2017	2977.3918	0.0000	1.0000
JC69IG	37	-1381.8652	2980.5794	0.0000	1.0000
SYM	40	-1376.9420	2988.3154	0.0000	1.0000
F81	38	-1388.0078	2998.7255	0.0000	1.0000
JC69	35	-1401.4843	3008.0962	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/chr17_3035.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3035.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/chr17_3035.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3035.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/chr17_3035.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3035.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

