ecceTERA 1.2.4 – Gene Tree Species Tree Reconciliation

ecceTERA 1.2.4

:: DESCRIPTION

Given a (dated) species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), ecceTERA computes the score of a most parsimonious reconciliation (MPR).

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ecceTERA

:: MORE INFORMATION

Citation

Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26. PMID: 27153713.

DupTree – Large Scale Gene Tree Parsimony Analysis

DupTree

:: DESCRIPTION

DupTree is a program for large-scale phylogenetic analyses using gene tree parsimony.The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

  DupTree

:: MORE INFORMATION

Citation

DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Andre Wehe, Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein.
Bioinformatics, 24(13): 1540-1541, 2008.

PolytomySolver 0.1 – Finds an Optimal Binary Resolution of the Gene Tree

PolytomySolver 0.1

:: DESCRIPTION

Given a non-binary gene tree and a binary species tree, PolytomySolver finds an optimal binary resolution of the gene tree such that the number of duplications + losses is minimized.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  PolytomySolver

:: MORE INFORMATION

Citation

Lafond M, Swenson KM, El-Mabrouk N:
An optimal reconciliation algorithm for gene trees with polytomies.
In WABI, volume 7534 of LNBI/LNBI; 2012:106-122.

PolytomySolverNAD 0.1 – Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees

PolytomySolverNAD 0.1

:: DESCRIPTION

Given a rooted binary gene tree and species tree, PolytomySolverNAD corrects a NAD (Non-Apparent Duplication) of the gene tree by applying multifurcation.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  PolytomySolverNAD

:: MORE INFORMATION

Citation

Polytomy refinement for the correction of dubious duplications in gene trees.
Lafond M, Chauve C, Dondi R, El-Mabrouk N.
Bioinformatics. 2014 Sep 1;30(17):i519-i526. doi: 10.1093/bioinformatics/btu463.

ParalogyCorrector – Gene Tree Correction

ParalogyCorrector

:: DESCRIPTION

Given a gene tree, a species tree and a list of gene pairs that are required to be orthologs, ParalogyCorrector finds a gene tree as close as possible to the original that satisfies these constraints under reconciliation.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  ParalogyCorrector

:: MORE INFORMATION

Citation

Lafond M, Semeria M, Swenson K M, Tannier E, El-Mabrouk N :
Gene tree correction guided by orthology
BMC Bioinformatics 14:S5I; 10.1186/1471-2105-14-S15-S5-T, 2013.

MulRF 1.2 – Phylogenetic Analysis using Multi-copy Gene Trees

MulRF 1.2

:: DESCRIPTION

MulRF is a platform-independent software program designed to infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

MulRF

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 MulRF

:: MORE INFORMATION

Citation

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.
Chaudhary R, Fernández-Baca D, Burleigh JG.
Bioinformatics. 2014 Oct 1. pii: btu648.

RefineTree – Gene Tree Correction software

RefineTree

:: DESCRIPTION

RefineTree is a gene tree correction software, based on resolving a multifurcated gene tree in a way minimizing the reconciliation distance with a given species tree.

::DEVELOPER

NADIA EL-MABROUK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome evolution-aware gene trees
E. Noutahi, M. Semeria, M. Lafond, J. Seguin, B. Boussau, L. Gueguen, N. El-Mabrouk and Eric Taniier,
submitted to PloS.Comp.Biol, 2015.

BUCKy 1.4.4 – Gene Tree Reconciliation with Bayesian Concordance Analysis

BUCKy 1.4.4

:: DESCRIPTION

BUCKy (Bayesian Untangling of Concordance Knots) is a free program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Instead, groups of genes sharing the same tree are detected (while accounting for uncertainty in gene tree estimates), and then combined to gain more resolution on their common tree. No assumption is made regarding the reason for discordance among gene trees.

::DEVELOPER

Cécile Ané Bret Larget

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C++ Compiler

:: DOWNLOAD

BUCKy

:: MORE INFORMATION

Citation

B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010).
BUCKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis.
Bioinformatics (2010) September 21, 2010 doi: 10.1093/bioinformatics/btq539

TreeFam r9 – Database of Animal Gene Trees

TreeFam r9

:: DESCRIPTION

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

::DEVELOPER

TreeFam team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic Acids Res. 2013 Nov 4

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.
TreeFam: a curated database of phylogenetic trees of animal gene families.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

SPIMAP 1.1 – Species Informed Maximum A Posteriori Gene Tree Reconstruction

SPIMAP 1.1

:: DESCRIPTION

SPIMAP is a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree.

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Python

:: DOWNLOAD

 SPIMAP 

:: MORE INFORMATION

Citation

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
Matthew D. Rasmussen and Manolis Kellis.
Mol Biol Evol (2011) 28 (1): 273-290.

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