research-article

STEM

Authors:

Laura S. Kubatko,

Bryan C. Carstens,

L. Lacey KnowlesAuthors Info & Claims

Bioinformatics, Volume 25, Issue 7

Pages 971 - 973

https://doi.org/10.1093/bioinformatics/btp079

Published: 01 April 2009 Publication History

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: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

Cited By

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Mahbub SSawmya SSaha AReaz RRahman MBayzid M(2022)QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing DataResearch in Computational Molecular Biology10.1007/978-3-031-04749-7_10(159-176)Online publication date: 22-May-2022
https://dl.acm.org/doi/10.1007/978-3-031-04749-7_10
Chelly Dagdia ZAvdeyev PBayzid M(2021)Biological computation and computational biology: survey, challenges, and discussionArtificial Intelligence Review10.1007/s10462-020-09951-154:6(4169-4235)Online publication date: 27-Jan-2021
https://dl.acm.org/doi/10.1007/s10462-020-09951-1
Du PNakhleh LShehu AWu CBoucher CLi JLiu HPop M(2018)Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence ModelProceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/3233547.3233600(376-385)Online publication date: 15-Aug-2018
https://dl.acm.org/doi/10.1145/3233547.3233600
Show More Cited By

STEM
1. Applied computing
  1. Life and medical sciences
2. Mathematics of computing
  1. Discrete mathematics
    1. Graph theory

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Published In

Bioinformatics Volume 25, Issue 7

April 2009

140 pages

ISSN:1367-4803

Issue’s Table of Contents

Publisher

Oxford University Press, Inc.

United States

Publication History

Published: 01 April 2009

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Mahbub SSawmya SSaha AReaz RRahman MBayzid M(2022)QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing DataResearch in Computational Molecular Biology10.1007/978-3-031-04749-7_10(159-176)Online publication date: 22-May-2022
https://dl.acm.org/doi/10.1007/978-3-031-04749-7_10
Chelly Dagdia ZAvdeyev PBayzid M(2021)Biological computation and computational biology: survey, challenges, and discussionArtificial Intelligence Review10.1007/s10462-020-09951-154:6(4169-4235)Online publication date: 27-Jan-2021
https://dl.acm.org/doi/10.1007/s10462-020-09951-1
Du PNakhleh LShehu AWu CBoucher CLi JLiu HPop M(2018)Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence ModelProceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/3233547.3233600(376-385)Online publication date: 15-Aug-2018
https://dl.acm.org/doi/10.1145/3233547.3233600
Bhattacharyya SMukhopadhyay J(2016)Accumulated Coalescence Rank and Excess Gene Count for Species Tree InferenceAlgorithms for Computational Biology10.1007/978-3-319-38827-4_8(93-105)Online publication date: 21-Jun-2016
https://dl.acm.org/doi/10.1007/978-3-319-38827-4_8
Wang WChang YWu CKang W(2012)A self-adaptive computing framework for parallel maximum likelihood evaluationThe Journal of Supercomputing10.1007/s11227-011-0648-761:1(67-83)Online publication date: 1-Jul-2012
https://dl.acm.org/doi/10.1007/s11227-011-0648-7
Lin HBurleigh JEulenstein O(2011)The deep coalescence consensus tree problem is Pareto on clustersProceedings of the 7th international conference on Bioinformatics research and applications10.5555/2009164.2009183(172-183)Online publication date: 27-May-2011
https://dl.acm.org/doi/10.5555/2009164.2009183
Yu YWarnow TNakhleh L(2011)Algorithms for MDC-based multi-locus phylogeny inferenceProceedings of the 15th Annual international conference on Research in computational molecular biology10.5555/1987587.1987634(531-545)Online publication date: 28-Mar-2011
https://dl.acm.org/doi/10.5555/1987587.1987634

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Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA

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MicroRNA sequence motifs reveal asymmetry between the stem arms

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