Downloads Phylogenomics

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Baobab

  

Baobab is an editor for large phylogenetic trees written in Java. ree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier. arge means that Baobab includes tools to simplify the task of managing heavy dataset (typically dealing with several hundred species).

Author(s)

Julien Dutheil


Version

3.31


Platform

Linux - Windows


Source

Yes


Downloads

0




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graphDTL

Phylogenetic reconstruction

  

Given a dated species tree S and a gene tree G, this program computes the graph reconciliation for G and S, according to the combinatorial model defined in [Celine Scornavacca, Wojciech Paprotny and Vincent Berry and Vincent Ranwez. Vol. 11, No. 2 (2013) 1250025 (19 pages) Journal of Bioinformatics and Computational Biology].

This work was partially supported by the IBC http://www.ibc-montpellier.fr/

Author(s)

Céline Scornavacca


Version

1


Platform

Linux


Source

Yes


Downloads

0


Subsections

Phylogenetic reconstruction


Tags

Bio++




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HGT_simul

  

HGT_simul implements the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press) The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes. The user can also control the geometry of the data set: number of taxa, number of genes, sequence lengths, and sampling effort. The input is a (rooted) species tree + an option file setting the parameters of the simulation. The output is a set of genes; for each gene, the simulated alignement and the underlying true gene tree are written in separate files.

Author(s)

Galtier N.


Version

1.2


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Tags

ISEM




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MACSE

Alignment

  

NEW MACSE version (1.01b)

MACSE now provides a full toolkit dedicated to coding sequence alignments. This toolkit allows us to reliably align thousands of COI and matK sequences in a barcoding context (see our barcoding subproject web page for further information). Here are some of the functionalities provided by the various subprograms included in MACSE: Enriching an existing alignment with additional sequences Refining an existing alignment Splitting an existing alignment keeping a subset of sites and/or sequences Formatting and exporting an alignment (e.g. by removing or masking codons containing frameshifts) Translating a nucleotide alignment into an amino acid alignment ... For usage examples see MACSE tutorial and download associated examples.
Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page: MACSE Webpage

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel DOUZERY


Version

1.01b


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Alignment




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Phylo_win

  

Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes and Cantor, Kimura, Tajima and Nei, HKY, Galtier and Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

Author(s)

Galtier, N., Gouy, M.


Version

2.0


Platform

Linux - Windows - Mac


Source

No


Downloads

0


Tags

ISEM




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PopPhyl

Tool

  

The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.

Executables tools

  • Reads2SNP C++ executable (Static compilation for 32, 64 bits Linux and binary for MacOS)(download)
  • dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)(download)
  • ORF extractor perl script (download)
Galaxy-related tools

Author(s)

Nicolas Galtier et al.


Version

1


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Tool - Mapping - Assembler


Tags

ISEM




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Sources

Expand all - Reduce all Items : 4 / 4

Number of results per page

Baobab

Baobab is an editor for large phylogenetic trees written in Java. ree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier. arge means that Baobab includes tools to simplify the task of managing heavy dataset (typically dealing with several hundred species). Java Development Kit version 1.4.2 minimum.

Langage

JAVA


Downloads

0


Tags

ISEM




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CoMap

A C++ shell program to detect co-evolving groups of sites CoMap performs the following tasks: - Compute probabilistic substitution maps - Test for pairs/groups of sites that do not evolve independently

Langage

C++


Downloads

0




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ecceTERA

ecceTERA: Tree Estimating using Reconciliation and Amalgamation
version 1.2.4, 14/09/2016
(formerly known as TERA)


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).
Additionally, ecceTERA will also compute either:

(1) a reconciliation graph describing all reconciliations for the species tree and each tree in G, according to the combinatorial model defined in [1], as well as the median reconciliations [3] and a random reconciliation (each reconciliation is outputted along with its score and event supports supports [3]), or (2) an MPR score for the “amalgamation” of all the gene trees in G (considered as unrooted), as well as an optimal gene tree according to the combinatorial model defined in [2].


[1] Celine Scornavacca, Wojciech Paprotny and Vincent Berry and Vincent Ranwez. Journal of Bioinformatics and Computational Biology Vol. 11, No. 2 (2013), p. 1250025.
[2] Celine Scornavacca, Edwin Jacox, and Gergely Szöllősi. Joint Amalgamation of Most Parsimonious Reconciled Gene Trees. Bioinformatics (2014): btu728.
[3] Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PloS One Vol. 8, No. 10 (2013), p. e73667.

Langage

C++


Downloads

0




download

HGT_simul

HGT_simul implements the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press) The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes. The user can also control the geometry of the data set: number of taxa, number of genes, sequence lengths, and sampling effort. The input is a (rooted) species tree + an option file setting the parameters of the simulation. The output is a set of genes; for each gene, the simulated alignement and the underlying true gene tree are written in separate files.

Langage

C++


Downloads

0


Tags

ISEM




download