
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:00 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_23687.phylip" (19 taxa, 475 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1221.6682	2530.8940	0.3044	0.3044
GTRG	44	-1217.0046	2531.2185	0.2588	0.5632
HKYIG	41	-1221.1457	2532.2452	0.1549	0.7181
GTRIG	45	-1216.4273	2532.5049	0.1360	0.8541
HKYI	40	-1222.8380	2533.2336	0.0945	0.9486
GTRI	44	-1218.6217	2534.4528	0.0514	1.0000
GTR	43	-1230.2450	2555.2696	0.0000	1.0000
HKY	39	-1235.0737	2555.3198	0.0000	1.0000
F81G	39	-1238.0819	2561.3362	0.0000	1.0000
F81IG	40	-1237.5980	2562.7536	0.0000	1.0000
F81I	39	-1239.0706	2563.3136	0.0000	1.0000
F81	38	-1251.6020	2586.0021	0.0000	1.0000
SYMG	41	-1260.3964	2610.7466	0.0000	1.0000
K2PG	37	-1267.2028	2614.8403	0.0000	1.0000
K2PIG	38	-1266.6686	2616.1354	0.0000	1.0000
K2PI	37	-1268.0819	2616.5986	0.0000	1.0000
SYMIG	42	-1262.8946	2618.1504	0.0000	1.0000
SYMI	41	-1264.3832	2618.7202	0.0000	1.0000
JC69G	36	-1276.0673	2630.2168	0.0000	1.0000
SYM	40	-1274.0292	2635.6159	0.0000	1.0000
JC69IG	37	-1278.3614	2637.1576	0.0000	1.0000
JC69I	36	-1279.7336	2637.5494	0.0000	1.0000
K2P	36	-1281.4450	2640.9722	0.0000	1.0000
JC69	35	-1289.2445	2654.2293	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1217.0046	2522.0092	0.3511	0.3511
GTRIG	45	-1216.4273	2522.8545	0.2301	0.5812
HKYG	40	-1221.6682	2523.3364	0.1808	0.7620
HKYIG	41	-1221.1457	2524.2914	0.1122	0.8742
GTRI	44	-1218.6217	2525.2435	0.0697	0.9439
HKYI	40	-1222.8380	2525.6760	0.0561	1.0000
GTR	43	-1230.2450	2546.4901	0.0000	1.0000
HKY	39	-1235.0737	2548.1474	0.0000	1.0000
F81G	39	-1238.0819	2554.1638	0.0000	1.0000
F81IG	40	-1237.5980	2555.1960	0.0000	1.0000
F81I	39	-1239.0706	2556.1412	0.0000	1.0000
F81	38	-1251.6020	2579.2040	0.0000	1.0000
SYMG	41	-1260.3964	2602.7928	0.0000	1.0000
K2PG	37	-1267.2028	2608.4056	0.0000	1.0000
K2PIG	38	-1266.6686	2609.3372	0.0000	1.0000
SYMIG	42	-1262.8946	2609.7893	0.0000	1.0000
K2PI	37	-1268.0819	2610.1638	0.0000	1.0000
SYMI	41	-1264.3832	2610.7663	0.0000	1.0000
JC69G	36	-1276.0673	2624.1346	0.0000	1.0000
SYM	40	-1274.0292	2628.0583	0.0000	1.0000
JC69IG	37	-1278.3614	2630.7228	0.0000	1.0000
JC69I	36	-1279.7336	2631.4672	0.0000	1.0000
K2P	36	-1281.4450	2634.8900	0.0000	1.0000
JC69	35	-1289.2445	2648.4890	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1221.6682	2689.8690	0.7202	0.7202
HKYI	40	-1222.8380	2692.2086	0.2236	0.9438
HKYIG	41	-1221.1457	2694.9873	0.0557	0.9995
GTRG	44	-1217.0046	2705.1950	0.0003	0.9999
GTRI	44	-1218.6217	2708.4293	0.0001	0.9999
GTRIG	45	-1216.4273	2710.2037	0.0000	1.0000
HKY	39	-1235.0737	2710.5166	0.0000	1.0000
F81G	39	-1238.0819	2716.5331	0.0000	1.0000
F81I	39	-1239.0706	2718.5105	0.0000	1.0000
F81IG	40	-1237.5980	2721.7286	0.0000	1.0000
GTR	43	-1230.2450	2725.5126	0.0000	1.0000
F81	38	-1251.6020	2737.4099	0.0000	1.0000
K2PG	37	-1267.2028	2762.4482	0.0000	1.0000
K2PI	37	-1268.0819	2764.2065	0.0000	1.0000
K2PIG	38	-1266.6686	2767.5432	0.0000	1.0000
SYMG	41	-1260.3964	2773.4887	0.0000	1.0000
JC69G	36	-1276.0673	2774.0140	0.0000	1.0000
JC69I	36	-1279.7336	2781.3465	0.0000	1.0000
SYMI	41	-1264.3832	2781.4622	0.0000	1.0000
SYMIG	42	-1262.8946	2784.6485	0.0000	1.0000
JC69IG	37	-1278.3614	2784.7655	0.0000	1.0000
K2P	36	-1281.4450	2784.7694	0.0000	1.0000
JC69	35	-1289.2445	2794.2050	0.0000	1.0000
SYM	40	-1274.0292	2794.5909	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_23687.phylip = 1 - 475;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23687.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23687.phylip = 1 - 475;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23687.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;


[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_23687.phylip = 1 - 475;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23687.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

