
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:46 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/chr2_25860.phylip" (19 taxa, 396 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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
HKYI	40	-962.1376	2013.5146	0.4733	0.4733
HKYG	40	-962.3977	2014.0349	0.3649	0.8381
HKYIG	41	-962.3976	2016.5240	0.1051	0.9432
GTRI	44	-960.6137	2020.5095	0.0143	0.9576
GTRG	44	-960.9019	2021.0858	0.0107	0.9683
K2PI	37	-969.7003	2021.2553	0.0099	0.9782
K2PG	37	-969.9320	2021.7187	0.0078	0.9860
GTRIG	45	-960.9017	2023.6319	0.0030	0.9890
F81I	39	-968.5450	2023.8541	0.0027	0.9917
HKY	39	-968.6153	2023.9946	0.0025	0.9942
K2PIG	38	-969.9318	2024.1660	0.0023	0.9965
F81G	39	-968.8019	2024.3679	0.0021	0.9986
F81IG	40	-968.8016	2026.8427	0.0006	0.9992
SYMI	41	-968.3556	2028.4401	0.0003	0.9995
SYMG	41	-968.5951	2028.9190	0.0002	0.9997
GTR	43	-967.1616	2031.0732	0.0001	0.9998
SYMIG	42	-968.5948	2031.4220	0.0001	0.9998
JC69I	36	-976.0373	2031.4953	0.0001	0.9999
K2P	36	-976.2412	2031.9030	0.0000	0.9999
JC69G	36	-976.2801	2031.9808	0.0000	1.0000
F81	38	-974.9606	2034.2236	0.0000	1.0000
JC69IG	37	-976.2798	2034.4143	0.0000	1.0000
SYM	40	-974.8895	2039.0185	0.0000	1.0000
JC69	35	-982.4380	2041.8761	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-962.1376	2004.2751	0.4421	0.4421
HKYG	40	-962.3977	2004.7955	0.3408	0.7829
HKYIG	41	-962.3976	2006.7951	0.1254	0.9083
GTRI	44	-960.6137	2009.2274	0.0372	0.9455
GTRG	44	-960.9019	2009.8037	0.0279	0.9733
GTRIG	45	-960.9017	2011.8033	0.0103	0.9836
K2PI	37	-969.7003	2013.4006	0.0046	0.9882
K2PG	37	-969.9320	2013.8640	0.0037	0.9918
F81I	39	-968.5450	2015.0901	0.0020	0.9938
HKY	39	-968.6153	2015.2306	0.0018	0.9957
F81G	39	-968.8019	2015.6039	0.0015	0.9972
K2PIG	38	-969.9318	2015.8635	0.0013	0.9985
F81IG	40	-968.8016	2017.6033	0.0006	0.9991
SYMI	41	-968.3556	2018.7113	0.0003	0.9994
SYMG	41	-968.5951	2019.1901	0.0003	0.9997
GTR	43	-967.1616	2020.3232	0.0001	0.9998
SYMIG	42	-968.5948	2021.1897	0.0001	0.9999
JC69I	36	-976.0373	2024.0747	0.0000	0.9999
K2P	36	-976.2412	2024.4824	0.0000	1.0000
JC69G	36	-976.2801	2024.5602	0.0000	1.0000
F81	38	-974.9606	2025.9211	0.0000	1.0000
JC69IG	37	-976.2798	2026.5596	0.0000	1.0000
SYM	40	-974.8895	2029.7791	0.0000	1.0000
JC69	35	-982.4380	2034.8761	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-969.7003	2160.7129	0.4181	0.4181
K2PG	37	-969.9320	2161.1763	0.3317	0.7498
HKYI	40	-962.1376	2163.5317	0.1021	0.8519
HKYG	40	-962.3977	2164.0520	0.0787	0.9307
K2PIG	38	-969.9318	2167.1573	0.0167	0.9474
JC69I	36	-976.0373	2167.4056	0.0147	0.9621
K2P	36	-976.2412	2167.8133	0.0120	0.9741
JC69G	36	-976.2801	2167.8911	0.0116	0.9856
HKYIG	41	-962.3976	2170.0331	0.0040	0.9896
F81I	39	-968.5450	2170.3652	0.0034	0.9930
HKY	39	-968.6153	2170.5058	0.0031	0.9961
F81G	39	-968.8019	2170.8790	0.0026	0.9987
JC69IG	37	-976.2798	2173.8719	0.0006	0.9992
JC69	35	-982.4380	2174.2256	0.0005	0.9997
F81IG	40	-968.8016	2176.8598	0.0001	0.9999
F81	38	-974.9606	2177.2148	0.0001	1.0000
SYMI	41	-968.3556	2181.9493	0.0000	1.0000
SYMG	41	-968.5951	2182.4281	0.0000	1.0000
GTRI	44	-960.6137	2184.4097	0.0000	1.0000
GTRG	44	-960.9019	2184.9859	0.0000	1.0000
SYMIG	42	-968.5948	2188.4091	0.0000	1.0000
SYM	40	-974.8895	2189.0356	0.0000	1.0000
GTRIG	45	-960.9017	2190.9670	0.0000	1.0000
GTR	43	-967.1616	2191.5240	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.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;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25860.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

