
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:46 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/chr7_11565.phylip" (19 taxa, 656 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: HKYIG


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
HKYIG	41	-2459.2642	5006.1375	0.7519	0.7519
GTRIG	45	-2456.5712	5009.9293	0.1129	0.8649
GTRG	44	-2457.7728	5010.0268	0.1076	0.9724
HKYG	40	-2463.7110	5012.7554	0.0275	0.9999
GTRI	44	-2465.3696	5025.2204	0.0001	1.0000
HKYI	40	-2471.0954	5027.5242	0.0000	1.0000
K2PIG	38	-2477.8792	5036.5622	0.0000	1.0000
K2PG	37	-2480.6413	5039.8328	0.0000	1.0000
K2PI	37	-2481.4250	5041.4001	0.0000	1.0000
SYMIG	42	-2476.6088	5043.1099	0.0000	1.0000
SYMG	41	-2478.3095	5044.2282	0.0000	1.0000
SYMI	41	-2485.5536	5058.7164	0.0000	1.0000
F81G	39	-2520.0800	5123.2250	0.0000	1.0000
F81IG	40	-2519.4252	5124.1837	0.0000	1.0000
F81I	39	-2527.3673	5137.7995	0.0000	1.0000
JC69G	36	-2535.3482	5147.0000	0.0000	1.0000
JC69IG	37	-2534.6022	5147.7545	0.0000	1.0000
HKY	39	-2537.1210	5157.3069	0.0000	1.0000
GTR	43	-2533.4363	5159.0556	0.0000	1.0000
JC69I	36	-2542.8176	5161.9388	0.0000	1.0000
K2P	36	-2556.4759	5189.2556	0.0000	1.0000
SYM	40	-2553.2887	5191.9107	0.0000	1.0000
F81	38	-2591.7773	5264.3586	0.0000	1.0000
JC69	35	-2607.5195	5289.1035	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2459.2642	5000.5284	0.6562	0.6562
GTRIG	45	-2456.5712	5003.1424	0.1776	0.8338
GTRG	44	-2457.7728	5003.5456	0.1452	0.9790
HKYG	40	-2463.7110	5007.4221	0.0209	0.9999
GTRI	44	-2465.3696	5018.7392	0.0001	1.0000
HKYI	40	-2471.0954	5022.1909	0.0000	1.0000
K2PIG	38	-2477.8792	5031.7583	0.0000	1.0000
K2PG	37	-2480.6413	5035.2826	0.0000	1.0000
K2PI	37	-2481.4250	5036.8499	0.0000	1.0000
SYMIG	42	-2476.6088	5037.2176	0.0000	1.0000
SYMG	41	-2478.3095	5038.6191	0.0000	1.0000
SYMI	41	-2485.5536	5053.1072	0.0000	1.0000
F81G	39	-2520.0800	5118.1601	0.0000	1.0000
F81IG	40	-2519.4252	5118.8503	0.0000	1.0000
F81I	39	-2527.3673	5132.7346	0.0000	1.0000
JC69G	36	-2535.3482	5142.6963	0.0000	1.0000
JC69IG	37	-2534.6022	5143.2044	0.0000	1.0000
HKY	39	-2537.1210	5152.2420	0.0000	1.0000
GTR	43	-2533.4363	5152.8726	0.0000	1.0000
JC69I	36	-2542.8176	5157.6351	0.0000	1.0000
K2P	36	-2556.4759	5184.9518	0.0000	1.0000
SYM	40	-2553.2887	5186.5773	0.0000	1.0000
F81	38	-2591.7773	5259.5547	0.0000	1.0000
JC69	35	-2607.5195	5285.0389	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2459.2642	5184.4610	0.7686	0.7686
HKYG	40	-2463.7110	5186.8685	0.2306	0.9993
GTRG	44	-2457.7728	5200.9367	0.0002	0.9995
K2PG	37	-2480.6413	5201.2705	0.0002	0.9996
HKYI	40	-2471.0954	5201.6373	0.0001	0.9998
K2PIG	38	-2477.8792	5202.2324	0.0001	0.9999
K2PI	37	-2481.4250	5202.8379	0.0001	1.0000
GTRIG	45	-2456.5712	5205.0197	0.0000	1.0000
GTRI	44	-2465.3696	5216.1303	0.0000	1.0000
SYMG	41	-2478.3095	5222.5517	0.0000	1.0000
SYMIG	42	-2476.6088	5225.6363	0.0000	1.0000
SYMI	41	-2485.5536	5237.0398	0.0000	1.0000
F81G	39	-2520.0800	5293.1204	0.0000	1.0000
F81IG	40	-2519.4252	5298.2968	0.0000	1.0000
JC69G	36	-2535.3482	5304.1981	0.0000	1.0000
F81I	39	-2527.3673	5307.6949	0.0000	1.0000
JC69IG	37	-2534.6022	5309.1923	0.0000	1.0000
JC69I	36	-2542.8176	5319.1369	0.0000	1.0000
HKY	39	-2537.1210	5327.2023	0.0000	1.0000
GTR	43	-2533.4363	5345.7776	0.0000	1.0000
K2P	36	-2556.4759	5346.4536	0.0000	1.0000
SYM	40	-2553.2887	5366.0238	0.0000	1.0000
F81	38	-2591.7773	5430.0288	0.0000	1.0000
JC69	35	-2607.5195	5442.0546	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip = 1 - 656;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip = 1 - 656;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip = 1 - 656;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

