title: Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.
abstract: BACKGROUND
  During the most recent decade many Bayesian statistical models and software for answering questions related to the genetic structure underlying population samples have appeared in the scientific literature. Most of these methods utilize molecular markers for the inferences, while some are also capable of handling DNA sequence data. In a number of earlier works, we have introduced an array of statistical methods for population genetic inference that are implemented in the software BAPS. However, the complexity of biological problems related to genetic structure analysis keeps increasing such that in many cases the current methods may provide either inappropriate or insufficient solutions.
  
  
  RESULTS
  We discuss the necessity of enhancing the statistical approaches to face the challenges posed by the ever-increasing amounts of molecular data generated by scientists over a wide range of research areas and introduce an array of new statistical tools implemented in the most recent version of BAPS. With these methods it is possible, e.g., to fit genetic mixture models using user-specified numbers of clusters and to estimate levels of admixture under a genetic linkage model. Also, alleles representing a different ancestry compared to the average observed genomic positions can be tracked for the sampled individuals, and a priori specified hypotheses about genetic population structure can be directly compared using Bayes' theorem. In general, we have improved further the computational characteristics of the algorithms behind the methods implemented in BAPS facilitating the analyses of large and complex datasets. In particular, analysis of a single dataset can now be spread over multiple computers using a script interface to the software.
  
  
  CONCLUSIONS
  The Bayesian modelling methods introduced in this article represent an array of enhanced tools for learning the genetic structure of populations. Their implementations in the BAPS software are designed to meet the increasing need for analyzing large-scale population genetics data. The software is freely downloadable for Windows, Linux and Mac OS X systems at http://web.abo.fi/fak/mnf//mate/jc/software/baps.html.
authors.affiliation: Department of Mathematics, Fänriksgatan 3B, Abo Akademi University, Abo, Finland. jukka.corander@abo.fi
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.forename: Pekka
authors.initials: P
authors.lastname: Marttinen
authors.forename: Jukka
authors.initials: J
authors.lastname: Sirén
authors.forename: Jing
authors.initials: J
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D000483:Alleles; D001499:Bayes Theorem; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D008040:Genetic Linkage; D040342:Genetic Structures; D005828:Genetics, Population; D006801:Humans; D008957:Models, Genetic; D011153:Population / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D013269:Stochastic Processes