
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:32 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/chr4_7006.phylip" (19 taxa, 379 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	-1236.6830	2573.2223	0.3011	0.3011
GTRIG	45	-1235.9660	2574.3644	0.1701	0.4713
SYMG	41	-1241.2384	2574.6963	0.1441	0.6154
K2PG	37	-1246.3800	2575.0064	0.1234	0.7388
SYMIG	42	-1240.5430	2575.8361	0.0815	0.8203
K2PIG	38	-1245.6651	2576.0479	0.0733	0.8936
GTRI	44	-1238.9381	2577.7324	0.0316	0.9252
HKYG	40	-1244.2060	2578.1162	0.0261	0.9513
SYMI	41	-1243.4273	2579.0741	0.0161	0.9674
HKYIG	41	-1243.4372	2579.0940	0.0160	0.9834
K2PI	37	-1248.5583	2579.3628	0.0140	0.9974
HKYI	40	-1246.5030	2582.7102	0.0026	1.0000
JC69G	36	-1267.3868	2614.5631	0.0000	1.0000
JC69IG	37	-1266.7665	2615.7792	0.0000	1.0000
F81G	39	-1265.1556	2617.5147	0.0000	1.0000
JC69I	36	-1269.4781	2618.7456	0.0000	1.0000
F81IG	40	-1264.5316	2618.7674	0.0000	1.0000
F81I	39	-1267.2148	2621.6330	0.0000	1.0000
SYM	40	-1266.7510	2623.2062	0.0000	1.0000
K2P	36	-1271.7257	2623.2408	0.0000	1.0000
GTR	43	-1263.2370	2623.7694	0.0000	1.0000
HKY	39	-1269.6346	2626.4727	0.0000	1.0000
JC69	35	-1292.1956	2661.7382	0.0000	1.0000
F81	38	-1290.1398	2664.9971	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1236.6830	2561.3660	0.4114	0.4114
GTRIG	45	-1235.9660	2561.9320	0.3100	0.7215
SYMG	41	-1241.2384	2564.4767	0.0869	0.8083
SYMIG	42	-1240.5430	2565.0861	0.0640	0.8724
GTRI	44	-1238.9381	2565.8761	0.0431	0.9155
K2PG	37	-1246.3800	2566.7601	0.0277	0.9433
K2PIG	38	-1245.6651	2567.3302	0.0209	0.9641
HKYG	40	-1244.2060	2568.4121	0.0121	0.9763
SYMI	41	-1243.4273	2568.8545	0.0097	0.9860
HKYIG	41	-1243.4372	2568.8745	0.0096	0.9956
K2PI	37	-1248.5583	2571.1165	0.0031	0.9988
HKYI	40	-1246.5030	2573.0061	0.0012	1.0000
JC69G	36	-1267.3868	2606.7736	0.0000	1.0000
JC69IG	37	-1266.7665	2607.5329	0.0000	1.0000
F81G	39	-1265.1556	2608.3112	0.0000	1.0000
F81IG	40	-1264.5316	2609.0633	0.0000	1.0000
JC69I	36	-1269.4781	2610.9561	0.0000	1.0000
F81I	39	-1267.2148	2612.4295	0.0000	1.0000
GTR	43	-1263.2370	2612.4739	0.0000	1.0000
SYM	40	-1266.7510	2613.5020	0.0000	1.0000
K2P	36	-1271.7257	2615.4513	0.0000	1.0000
HKY	39	-1269.6346	2617.2691	0.0000	1.0000
JC69	35	-1292.1956	2654.3912	0.0000	1.0000
F81	38	-1290.1398	2656.2795	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1246.3800	2712.4489	0.8189	0.8189
K2PI	37	-1248.5583	2716.8053	0.0927	0.9116
K2PIG	38	-1245.6651	2716.9566	0.0860	0.9976
HKYG	40	-1244.2060	2725.9135	0.0010	0.9986
SYMG	41	-1241.2384	2725.9157	0.0010	0.9996
SYMI	41	-1243.4273	2730.2935	0.0001	0.9997
HKYIG	41	-1243.4372	2730.3134	0.0001	0.9998
SYMIG	42	-1240.5430	2730.4626	0.0001	0.9999
HKYI	40	-1246.5030	2730.5075	0.0001	1.0000
GTRG	44	-1236.6830	2734.6176	0.0000	1.0000
GTRIG	45	-1235.9660	2739.1211	0.0000	1.0000
GTRI	44	-1238.9381	2739.1277	0.0000	1.0000
JC69G	36	-1267.3868	2748.5249	0.0000	1.0000
JC69I	36	-1269.4781	2752.7074	0.0000	1.0000
JC69IG	37	-1266.7665	2753.2217	0.0000	1.0000
K2P	36	-1271.7257	2757.2026	0.0000	1.0000
F81G	39	-1265.1556	2761.8751	0.0000	1.0000
F81I	39	-1267.2148	2765.9934	0.0000	1.0000
F81IG	40	-1264.5316	2766.5647	0.0000	1.0000
HKY	39	-1269.6346	2770.8330	0.0000	1.0000
SYM	40	-1266.7510	2771.0035	0.0000	1.0000
GTR	43	-1263.2370	2781.7880	0.0000	1.0000
JC69	35	-1292.1956	2792.2050	0.0000	1.0000
F81	38	-1290.1398	2805.9059	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/chr4_7006.phylip = 1 - 379;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7006.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/chr4_7006.phylip = 1 - 379;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7006.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/chr4_7006.phylip = 1 - 379;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7006.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

