
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:30 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_3099.phylip" (19 taxa, 323 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	-1084.5599	2271.3644	0.3834	0.3834
GTRI	44	-1085.3007	2272.8460	0.1828	0.5662
HKYG	40	-1090.6507	2272.9327	0.1750	0.7412
GTRIG	45	-1084.3737	2273.6933	0.1197	0.8609
HKYI	40	-1091.3983	2274.4278	0.0829	0.9438
HKYIG	41	-1090.4735	2275.2033	0.0562	1.0000
K2PG	37	-1106.6023	2297.0712	0.0000	1.0000
K2PIG	38	-1106.3450	2299.1265	0.0000	1.0000
K2PI	37	-1107.6597	2299.1861	0.0000	1.0000
SYMG	41	-1103.2684	2300.7930	0.0000	1.0000
SYMI	41	-1104.1776	2302.6114	0.0000	1.0000
SYMIG	42	-1103.0098	2302.9196	0.0000	1.0000
GTR	43	-1107.7894	2315.1415	0.0000	1.0000
HKY	39	-1114.3072	2317.6392	0.0000	1.0000
F81G	39	-1123.0057	2335.0361	0.0000	1.0000
F81I	39	-1123.9188	2336.8622	0.0000	1.0000
F81IG	40	-1122.8209	2337.2731	0.0000	1.0000
K2P	36	-1132.9443	2347.2034	0.0000	1.0000
SYM	40	-1129.7556	2351.1423	0.0000	1.0000
JC69G	36	-1138.0237	2357.3621	0.0000	1.0000
JC69I	36	-1139.0070	2359.3288	0.0000	1.0000
JC69IG	37	-1137.8098	2359.4863	0.0000	1.0000
F81	38	-1146.8494	2380.1354	0.0000	1.0000
JC69	35	-1163.2778	2405.3361	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1084.5599	2257.1198	0.4638	0.4638
GTRI	44	-1085.3007	2258.6014	0.2211	0.6849
GTRIG	45	-1084.3737	2258.7475	0.2055	0.8904
HKYG	40	-1090.6507	2261.3015	0.0573	0.9477
HKYI	40	-1091.3983	2262.7966	0.0271	0.9748
HKYIG	41	-1090.4735	2262.9471	0.0252	1.0000
K2PG	37	-1106.6023	2287.2046	0.0000	1.0000
SYMG	41	-1103.2684	2288.5368	0.0000	1.0000
K2PIG	38	-1106.3450	2288.6899	0.0000	1.0000
K2PI	37	-1107.6597	2289.3195	0.0000	1.0000
SYMIG	42	-1103.0098	2290.0196	0.0000	1.0000
SYMI	41	-1104.1776	2290.3552	0.0000	1.0000
GTR	43	-1107.7894	2301.5788	0.0000	1.0000
HKY	39	-1114.3072	2306.6145	0.0000	1.0000
F81G	39	-1123.0057	2324.0114	0.0000	1.0000
F81IG	40	-1122.8209	2325.6419	0.0000	1.0000
F81I	39	-1123.9188	2325.8375	0.0000	1.0000
K2P	36	-1132.9443	2337.8887	0.0000	1.0000
SYM	40	-1129.7556	2339.5111	0.0000	1.0000
JC69G	36	-1138.0237	2348.0474	0.0000	1.0000
JC69IG	37	-1137.8098	2349.6196	0.0000	1.0000
JC69I	36	-1139.0070	2350.0141	0.0000	1.0000
F81	38	-1146.8494	2369.6988	0.0000	1.0000
JC69	35	-1163.2778	2396.5556	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1090.6507	2412.4076	0.6462	0.6462
HKYI	40	-1091.3983	2413.9027	0.3060	0.9522
HKYIG	41	-1090.4735	2417.8308	0.0429	0.9951
GTRG	44	-1084.5599	2423.3365	0.0027	0.9979
GTRI	44	-1085.3007	2424.8181	0.0013	0.9992
K2PG	37	-1106.6023	2426.9777	0.0004	0.9996
GTRIG	45	-1084.3737	2428.7419	0.0002	0.9998
K2PI	37	-1107.6597	2429.0926	0.0002	1.0000
K2PIG	38	-1106.3450	2432.2407	0.0000	1.0000
SYMG	41	-1103.2684	2443.4205	0.0000	1.0000
SYMI	41	-1104.1776	2445.2389	0.0000	1.0000
SYMIG	42	-1103.0098	2448.6810	0.0000	1.0000
HKY	39	-1114.3072	2453.9429	0.0000	1.0000
GTR	43	-1107.7894	2464.0178	0.0000	1.0000
F81G	39	-1123.0057	2471.3398	0.0000	1.0000
F81I	39	-1123.9188	2473.1659	0.0000	1.0000
K2P	36	-1132.9443	2473.8842	0.0000	1.0000
F81IG	40	-1122.8209	2476.7480	0.0000	1.0000
JC69G	36	-1138.0237	2484.0429	0.0000	1.0000
JC69I	36	-1139.0070	2486.0096	0.0000	1.0000
JC69IG	37	-1137.8098	2489.3928	0.0000	1.0000
SYM	40	-1129.7556	2490.6172	0.0000	1.0000
F81	38	-1146.8494	2513.2496	0.0000	1.0000
JC69	35	-1163.2778	2528.7735	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_3099.phylip = 1 - 323;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3099.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_3099.phylip = 1 - 323;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3099.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_3099.phylip = 1 - 323;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3099.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

