STEM: species tree estimation using maximum likelihood for gene trees under coalescence.
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.
Kubatko
Laura S
LS
Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA. lkubatko@stat.osu.edu
Carstens
Bryan C
BC
Knowles
L Lacey
LL
D000465:Algorithms; D003198:Computer Simulation; D005796:Genes; D016013:Likelihood Functions; D010802:Phylogeny; D012984:Software