title: STEM: species tree estimation using maximum likelihood for gene trees under coalescence.
abstract: STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree.
  
  
  BACKGROUND
  The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA. lkubatko@stat.osu.edu
authors.forename: Laura S
authors.initials: LS
authors.lastname: Kubatko
authors.forename: Bryan C
authors.initials: BC
authors.lastname: Carstens
authors.forename: L Lacey
authors.initials: LL
authors.lastname: Knowles
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005796:Genes; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software