Skip Navigation


Bioinformatics Advance Access originally published online on February 10, 2009
Bioinformatics 2009 25(7):971-973; doi:10.1093/bioinformatics/btp079
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
25/7/971    most recent
btp079v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Kubatko, L. S.
Right arrow Articles by Knowles, L. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kubatko, L. S.
Right arrow Articles by Knowles, L. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

Laura S. Kubatko 1,*, Bryan C. Carstens 2 and L. Lacey Knowles 3

1Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, 2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 and 3Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.

Contact: lkubatko{at}stat.osu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on November 28, 2008; revised on February 4, 2009; accepted on February 4, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Syst BiolHome page
B. C. O'Meara
New Heuristic Methods for Joint Species Delimitation and Species Tree Inference
Syst Biol, November 10, 2009; (2009) syp077v1.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. E. McCormack, H. Huang, and L. L. Knowles
Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design
Syst Biol, October 1, 2009; 58(5): 501 - 508.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
H. Huang and L. L. Knowles
What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
Syst Biol, October 1, 2009; 58(5): 527 - 536.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
L. S. Kubatko
Identifying Hybridization Events in the Presence of Coalescence via Model Selection
Syst Biol, October 1, 2009; 58(5): 478 - 488.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
L. L. Knowles
Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes
Syst Biol, October 1, 2009; 58(5): 463 - 467.
[Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.