L 2002, he has studied molecular evolution (including population genetics), mainly focusing on homology-based computational analyses of DNA and protein sequences. For more detailed information, including the list of his publications, refer to his ORCID record [52]. Competing interests The author declares that he has no competing interests. Consent for publication Not applicable. Ethics approval and consent to participate Not applicable. Received: 2 March 2016 Accepted: 26 May 2016 Published: 17 September 2016 References 1. Graur D, Li WH. Fundamentals of Molecular Evolution. 2nd ed. Sunderland: Sinauer Associates; 2000. 2. Gascuel O, editor. Mathematics of Evolution and Phylogeny. New York: Oxford University Press; 2005. 3. Lynch M. The Origins of Genome Architecture. Sunderland: Sinauer Associates; 2007. 4. Britten RJ. Divergence between samples of chimpanzee and human DNA AZD-8055 web sequences is 5 , counting indels. P Natl Acad Sci USA. 2002;99:13633?. 5. Britten RJ, Rowen L, Willians J, Cameron RA. Majority of divergence between closely related DNA samples is due to indels. P Natl Acad Sci USA. 2003;100:4661?. 6. The International Chimpanzee Chromosome 22 Consotrium. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004;429:382?. 7. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005;437:69?7. 8. Bishop MJ, Thompson EA. Maximum likelihood alignment of DNA sequences. J Mol Biol. 1986;190:159?5. 9. Thorne JL, Kishino H, Felsenstein J. An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol. 1991;33:114?4. 10. Rivas E. Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics. 2005;6:63. 11. Bradley RK, Holmes I. Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics. 2007;23:3258?2. 12. Mikl I, Nov ? Satija R, Lyngs?R, Hein J. Stochastic models of sequence evolution including insertion-deletion events. Stat Methods Med Res. 2009;18:453?5. 13. Holmes I, Bruno WJ. Evolutionary HMMs: a Bayesian approach to multiple sequence alignment. Bioinformatics. 2001;17:803?0.14. Holmes I. Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics. 2003;19:i147?7. 15. Bouchard-C ?A. A note on probabilistic models over strings: The linear algebra approach. Bull Math Biol. 2013;75:2529?0. 16. Herman JL, Nov ? Lyngs?R, Szab?A, Mikl I, Hein J. Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics. 2015;16:108. 17. Thorne JL, Kishino H, Felsenstein J. Inching toward reality: an improved likelihood model of sequence evolution. J Mol Evol. 1992;34:3?6. 18. Mikl I, Toroczkai Z. An improved model for statistical alignment. In: Gascuel O, Moret BME, editors. WABI 2001, LNCS 2249. Heidelberg: Splinger-Verlag; 2001. 19. Cartwright RA. Problems and solutions for estimating indel rates and length distribution. Mol Biol Evol. 2009;26:473?0. 20. Lunter PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26024392 G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res. 2008;18:298?09. 21. Mikl I, Lunter GA, Holmes I. A “long indel” model for evolutionary sequence alignment. Mol Biol Evol. 2004;21:529?0. 22. Kim J, Sinha S. Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alig.