
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:13 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/chr1_28786.phylip" (19 taxa, 342 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYG
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
HKYG	40	-936.1108	1963.1185	0.4023	0.4023
HKYIG	41	-935.0446	1963.5691	0.3211	0.7234
HKYI	40	-936.4953	1963.8875	0.2738	0.9972
GTRG	44	-936.6653	1974.6640	0.0013	0.9985
GTRIG	45	-935.8060	1975.5984	0.0008	0.9992
GTRI	44	-937.1729	1975.6792	0.0008	1.0000
K2PIG	38	-955.9796	1997.7413	0.0000	1.0000
K2PG	37	-957.3229	1997.8959	0.0000	1.0000
K2PI	37	-957.6772	1998.6043	0.0000	1.0000
F81G	39	-956.8686	2002.0682	0.0000	1.0000
F81IG	40	-955.8118	2002.5206	0.0000	1.0000
F81I	39	-957.2713	2002.8737	0.0000	1.0000
SYMIG	42	-953.8700	2003.8202	0.0000	1.0000
SYMG	41	-955.3231	2004.1263	0.0000	1.0000
SYMI	41	-955.7050	2004.8901	0.0000	1.0000
HKY	39	-959.0861	2006.5033	0.0000	1.0000
GTR	43	-958.9014	2016.5008	0.0000	1.0000
JC69G	36	-972.1775	2025.0894	0.0000	1.0000
JC69IG	37	-970.9787	2025.2074	0.0000	1.0000
JC69I	36	-972.5655	2025.8654	0.0000	1.0000
K2P	36	-980.4164	2041.5672	0.0000	1.0000
F81	38	-979.0576	2043.8974	0.0000	1.0000
SYM	40	-978.3711	2047.6391	0.0000	1.0000
JC69	35	-994.6045	2067.4442	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-935.0446	1952.0891	0.3850	0.3850
HKYG	40	-936.1108	1952.2215	0.3603	0.7453
HKYI	40	-936.4953	1952.9905	0.2453	0.9906
GTRG	44	-936.6653	1961.3307	0.0038	0.9944
GTRIG	45	-935.8060	1961.6119	0.0033	0.9977
GTRI	44	-937.1729	1962.3459	0.0023	1.0000
K2PIG	38	-955.9796	1987.9591	0.0000	1.0000
K2PG	37	-957.3229	1988.6459	0.0000	1.0000
K2PI	37	-957.6772	1989.3543	0.0000	1.0000
F81IG	40	-955.8118	1991.6236	0.0000	1.0000
F81G	39	-956.8686	1991.7371	0.0000	1.0000
SYMIG	42	-953.8700	1991.7400	0.0000	1.0000
F81I	39	-957.2713	1992.5425	0.0000	1.0000
SYMG	41	-955.3231	1992.6463	0.0000	1.0000
SYMI	41	-955.7050	1993.4101	0.0000	1.0000
HKY	39	-959.0861	1996.1722	0.0000	1.0000
GTR	43	-958.9014	2003.8028	0.0000	1.0000
JC69IG	37	-970.9787	2015.9574	0.0000	1.0000
JC69G	36	-972.1775	2016.3550	0.0000	1.0000
JC69I	36	-972.5655	2017.1310	0.0000	1.0000
K2P	36	-980.4164	2032.8327	0.0000	1.0000
F81	38	-979.0576	2034.1153	0.0000	1.0000
SYM	40	-978.3711	2036.7421	0.0000	1.0000
JC69	35	-994.6045	2059.2089	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-936.1108	2105.6139	0.5441	0.5441
HKYI	40	-936.4953	2106.3830	0.3704	0.9145
HKYIG	41	-935.0446	2109.3164	0.0855	1.0000
GTRG	44	-936.6653	2130.0623	0.0000	1.0000
K2PG	37	-957.3229	2130.5339	0.0000	1.0000
GTRI	44	-937.1729	2131.0776	0.0000	1.0000
K2PI	37	-957.6772	2131.2423	0.0000	1.0000
K2PIG	38	-955.9796	2133.6819	0.0000	1.0000
GTRIG	45	-935.8060	2134.1784	0.0000	1.0000
F81G	39	-956.8686	2141.2947	0.0000	1.0000
F81I	39	-957.2713	2142.1002	0.0000	1.0000
F81IG	40	-955.8118	2145.0160	0.0000	1.0000
HKY	39	-959.0861	2145.7298	0.0000	1.0000
SYMG	41	-955.3231	2149.8735	0.0000	1.0000
SYMI	41	-955.7050	2150.6373	0.0000	1.0000
SYMIG	42	-953.8700	2152.8020	0.0000	1.0000
JC69G	36	-972.1775	2154.4082	0.0000	1.0000
JC69I	36	-972.5655	2155.1841	0.0000	1.0000
JC69IG	37	-970.9787	2157.8454	0.0000	1.0000
GTR	43	-958.9014	2168.6997	0.0000	1.0000
K2P	36	-980.4164	2170.8859	0.0000	1.0000
F81	38	-979.0576	2179.8381	0.0000	1.0000
SYM	40	-978.3711	2190.1346	0.0000	1.0000
JC69	35	-994.6045	2193.4273	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/chr1_28786.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28786.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28786.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28786.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;


[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/chr1_28786.phylip = 1 - 342;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28786.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;


-------------------------------------------------------------
End of Output

