Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model

Systematic Biology

Volumn 61, Issue 6, 2012, Pages 927-940

  Zou, Liwen ^a   Susko, Edward ^b   Field, Chris ^b   Roger, Andrew J ^c  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b DALHOUSIE UNIVERSITY   (Canada)

^c DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Average substitutions; BH model; identifiability; nonstationary; NSGTR model

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; GENETIC HETEROGENEITY; GENETICS; MOLECULAR EVOLUTION; PLASMODIUM; STATISTICAL MODEL;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETIC HETEROGENEITY; MODELS, GENETIC; MODELS, STATISTICAL; PLASMODIUM;

EID: 84868017921     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys046     Document Type: Article

References (22)

1. Ababneh F., Jermiin L.S., Ma C., Robinson J. 2006. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics 22:1225-1231.
2. Allman E., Ane C., Rhodes JA. 2008. Identifiability of a Markovian model of molecular evolution with gamma-distributed rates. Adv. Appl. Prob. 40:229-249.
3. Barry D., Hartigan JA. 1987. Statistical analysis of hominoid molecular evolution. Stat. Sci. 2:191-210.
4. Boussau B., Gouy M. 2006. Efficient likelihood computations with nonreversible models of evolution. Syst. Biol. 55:756-768.
5. Chang J.T. 1996. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency Math. Biosci. 137: 51-73.
6. Davalos L.M., Perkins S.L. 2008. Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics 91: 433-442.
7. Dutheil J., Boussau B. 2008. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol. Biol. 8:255.
8. Felsenstein J. 2004. Inferring phylogenies. Sunderland Massachuetts (MA): Sinauer Associates, Inc.
9. Fletcher W., Yang Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26:1879-1888.
10. Foster P.G. 2004. Modeling compositional heterogeneity Syst. Biol. 53:485-495.
11. Foster P.G., Hickey DA. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290.
12. Galtier N., Gouy M. 1998. Inferring pattern and process: maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879.
13. Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
14. Hasegawa M., Kishino H., Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
15. Jayaswal V., Jermiin L., Robinson J. 2005. Estimation of phylogeny using a general Markov model. Evol. Bioinf. Online 1:62-80.
16. Jayaswal V., Jermiin L.S., Poladian L., Robinson J. 2011. Two stationary nonhomogeneous markov models of nucleotide sequence evolution. Syst. Biol. 60:74-86.
17. Minin V.N., Suchard M.A. 2008. Fast, accurate and simulation-free stochastic mapping. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 363:3985-3995.
18. Oscamou M., McDonald D., Yap V.B., Huttley G.A., Lladser M.E., Knight R. 2008. Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinformatics 9:511.
19. Sumner J.G., Fernández-Sánchez J., Jarvis P.D. 2012. Lie markov models. J. Theor. Biol. 298:16-31.
20. Tamura K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol. Biol. Evol. 9:678-687.
21. Yang Z., Roberts D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12: 451-458.
22. Zou L., Susko E., Field C., Roger A.J. 2011. The parameters of the Barry and Hartigan general Markov model are statistically nonidentifiable. Syst. Biol. 60:872-875.