DTL-RnB – Summarizing the Space of DTL Reconciliations

DTL-RnB

:: DESCRIPTION

DTL-RnB (Reconciliation Browser) is a tool for browsing the potentially large landscape of maximum parsimony reconciliations (MPRs) of pairs of phylogenetic trees (e.g., species and gene trees or host and parasite trees).

::DEVELOPER

DTL-RnB team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations.
Ma W, Smirnov D, Forman J, Schweickart A, Slocum C, Srinivasan S, Libeskind-Hadas R.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar 2

GraphDTL v004 – Graph Reconciliation for Species Tree S and Gene Tree G

GraphDTL v004

:: DESCRIPTION

GraphDTL is the first method to infer supports for evolutionary events based on their frequencies in the set of equally parsimonious reconciliations
Given a , this program computes

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GraphDTL

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28.
Representing a set of reconciliations in a compact way.
Scornavacca C1, Paprotny W, Berry V, Ranwez V.

SylvX 1.3 – A Viewer for Phylogenetic Tree Reconciliations

SylvX  1.3

:: DESCRIPTION

SylvX is a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

SylvX

:: REQUIREMENTS

  • Windows/ MacOsX

:: DOWNLOAD

  SylvX

:: MORE INFORMATION

Citation

SylvX: a viewer for phylogenetic tree reconciliations.
Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V.
Bioinformatics. 2015 Oct 29. pii: btv625

TERA 1.1 – Tree Estimating using Reconciliation and Amalgamation

TERA 1.1

:: 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), TERA computes the score of a most parsimonious reconciliation (MPR).

::DEVELOPER

Institut des Sciences de l’Evolution de Montpellier (ISEM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 TERA

:: MORE INFORMATION

Citation

Joint Amalgamation of Most Parsimonious Reconciled Gene Trees.
Scornavacca C, Jacox E, Szöllősi GJ.
Bioinformatics. 2014 Nov 6. pii: btu728.

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

Mowgli – Phylogenetic Tree Reconciliation Program

Mowgli

:: DESCRIPTION

Mowgli is a program for gene/species trees reconciliation analysis developed in C++. It is based on the model and algorithm of Doyon et al. [1] and the parsimony criterion: it seeks a Most Parsimonious Reconciliation (MPR for short) that explains the evolution of the gene family in terms of Duplications, Transfers, Losses, and Speciations (respectively denoted D, T, L, and S).Mowgli also takes into consideration uncertainty in the gene tree.

::DEVELOPER

South of France bioinformatics platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

  Mowgli

:: MORE INFORMATION

Citation:

J-P. Doyon, C. Scornavacca, K. Y. Gorbunov, G. Szollosi, V. Ranwez, and V. Berry.
An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers.
Lecture Notes in Computer Science, 2011, Volume 6398/2011, 93-108, DOI: 10.1007/978-3-642-16181-0_9

Xscape – Tools for Maximum-Parsimony Phylogenetic Tree Reconciliation over the Event Cost Landscape

Xscape

:: DESCRIPTION

Xscape is a set of Python tools for maximum parsimony phylogenetic event-based tree reconciliation in undated trees using the DTL (duplication-loss-transfer) model with applications to gene trees and species trees; parasite trees and host trees; and species trees and area cladograms.

::DEVELOPER

Ran Libeskind-Hadas

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python
  • matplotlib
  • BioPython

:: DOWNLOAD

 Xscape

:: MORE INFORMATION

Citation

Pareto-optimal phylogenetic tree reconciliation.
Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M.
Bioinformatics. 2014 Jun 15;30(12):i87-i95. doi: 10.1093/bioinformatics/btu289.

DeCoLT – Lateral Gene Transfer, Rearrangement, Reconciliation

DeCoLT

:: DESCRIPTION

The software DeCoLT computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications, losses and lateral gene transfer. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) reconciled gene trees which leaves are the extant genes.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

DeCoLT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.
Lateral gene transfer, rearrangement, reconciliation.
Patterson M, Szöllősi G, Daubin V, Tannier E.

gtp 0.15 – Gene Tree / Species Tree Reconciliation and Gene Tree Parsimony

gtp 0.15

:: DESCRIPTION

gtp is a software to infer gene duplication and speciation events on a gene tree.

::DEVELOPER

Mike Sanderson’s Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 gtp

:: MORE INFORMATION

Citation

A simple algorithm to infer gene duplication and speciation events on a gene tree.
Zmasek CM, Eddy SR.
Bioinformatics. 2001 Sep;17(9):821-8.