
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:49 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_17448.phylip" (19 taxa, 371 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	-1226.6316	2553.4104	0.3972	0.3972
GTRI	44	-1226.8650	2553.8772	0.3145	0.7118
GTRIG	45	-1226.6314	2556.0012	0.1088	0.8205
HKYI	40	-1233.2613	2556.4620	0.0864	0.9069
HKYG	40	-1233.4352	2556.8097	0.0726	0.9795
HKYIG	41	-1233.4350	2559.3381	0.0205	1.0000
K2PI	37	-1246.5810	2575.6064	0.0000	1.0000
K2PG	37	-1247.0435	2576.5315	0.0000	1.0000
K2PIG	38	-1247.0434	2579.0145	0.0000	1.0000
SYMI	41	-1243.3972	2579.2625	0.0000	1.0000
SYMG	41	-1243.8640	2580.1960	0.0000	1.0000
SYMIG	42	-1243.8639	2582.7400	0.0000	1.0000
GTR	43	-1250.5512	2598.6743	0.0000	1.0000
F81I	39	-1256.8380	2601.1019	0.0000	1.0000
F81G	39	-1257.3156	2602.0572	0.0000	1.0000
HKY	39	-1257.5193	2602.4645	0.0000	1.0000
F81IG	40	-1257.3155	2604.5703	0.0000	1.0000
JC69I	36	-1267.9524	2615.8809	0.0000	1.0000
JC69G	36	-1268.5344	2617.0449	0.0000	1.0000
JC69IG	37	-1268.5343	2619.5131	0.0000	1.0000
K2P	36	-1272.0304	2624.0369	0.0000	1.0000
SYM	40	-1267.9751	2625.8895	0.0000	1.0000
F81	38	-1281.0060	2646.9397	0.0000	1.0000
JC69	35	-1292.8210	2663.1644	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1226.6316	2541.2632	0.4320	0.4320
GTRI	44	-1226.8650	2541.7299	0.3421	0.7741
GTRIG	45	-1226.6314	2543.2627	0.1590	0.9330
HKYI	40	-1233.2613	2546.5226	0.0311	0.9642
HKYG	40	-1233.4352	2546.8703	0.0262	0.9904
HKYIG	41	-1233.4350	2548.8700	0.0096	1.0000
K2PI	37	-1246.5810	2567.1619	0.0000	1.0000
K2PG	37	-1247.0435	2568.0871	0.0000	1.0000
SYMI	41	-1243.3972	2568.7944	0.0000	1.0000
SYMG	41	-1243.8640	2569.7280	0.0000	1.0000
K2PIG	38	-1247.0434	2570.0868	0.0000	1.0000
SYMIG	42	-1243.8639	2571.7278	0.0000	1.0000
GTR	43	-1250.5512	2587.1024	0.0000	1.0000
F81I	39	-1256.8380	2591.6759	0.0000	1.0000
F81G	39	-1257.3156	2592.6312	0.0000	1.0000
HKY	39	-1257.5193	2593.0385	0.0000	1.0000
F81IG	40	-1257.3155	2594.6309	0.0000	1.0000
JC69I	36	-1267.9524	2607.9048	0.0000	1.0000
JC69G	36	-1268.5344	2609.0689	0.0000	1.0000
JC69IG	37	-1268.5343	2611.0686	0.0000	1.0000
SYM	40	-1267.9751	2615.9501	0.0000	1.0000
K2P	36	-1272.0304	2616.0609	0.0000	1.0000
F81	38	-1281.0060	2638.0120	0.0000	1.0000
JC69	35	-1292.8210	2655.6420	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1233.2613	2703.1707	0.5225	0.5225
HKYG	40	-1233.4352	2703.5184	0.4392	0.9617
HKYIG	41	-1233.4350	2709.4343	0.0228	0.9845
K2PI	37	-1246.5810	2712.0614	0.0061	0.9906
K2PG	37	-1247.0435	2712.9865	0.0039	0.9945
GTRG	44	-1226.6316	2713.5761	0.0029	0.9974
GTRI	44	-1226.8650	2714.0428	0.0023	0.9996
K2PIG	38	-1247.0434	2718.9025	0.0002	0.9998
GTRIG	45	-1226.6314	2719.4918	0.0001	1.0000
SYMI	41	-1243.3972	2729.3587	0.0000	1.0000
SYMG	41	-1243.8640	2730.2922	0.0000	1.0000
SYMIG	42	-1243.8639	2736.2083	0.0000	1.0000
F81I	39	-1256.8380	2744.4078	0.0000	1.0000
F81G	39	-1257.3156	2745.3631	0.0000	1.0000
HKY	39	-1257.5193	2745.7704	0.0000	1.0000
JC69I	36	-1267.9524	2748.8881	0.0000	1.0000
JC69G	36	-1268.5344	2750.0522	0.0000	1.0000
F81IG	40	-1257.3155	2751.2790	0.0000	1.0000
GTR	43	-1250.5512	2755.4991	0.0000	1.0000
JC69IG	37	-1268.5343	2755.9681	0.0000	1.0000
K2P	36	-1272.0304	2757.0441	0.0000	1.0000
SYM	40	-1267.9751	2772.5982	0.0000	1.0000
F81	38	-1281.0060	2786.8276	0.0000	1.0000
JC69	35	-1292.8210	2792.7091	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_17448.phylip = 1 - 371;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17448.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_17448.phylip = 1 - 371;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17448.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/chr3_17448.phylip = 1 - 371;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17448.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

