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Baobab |
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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 reconstructionpermalink |
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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/
Céline Scornavacca
Version
1
Platform
Linux
Source
Yes
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0
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HGT_simul |
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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
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MACSE |
Alignmentpermalink |
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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
Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel DOUZERY
Version
1.01b
Platform
Linux - Windows - Mac
Source
Yes
Downloads
0
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Phylo_win |
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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
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0
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PopPhyl |
Toolpermalink |
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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)
- All Galaxy-related wrappers/scripts(download)
Nicolas Galtier et al.
Version
1
Platform
Linux - Windows - Mac
Source
Yes
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Baobabpermalink |
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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.
LangageJAVA
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CoMappermalink |
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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
LangageC++
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0
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ecceTERApermalink |
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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.
C++
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HGT_simulpermalink |
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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.
LangageC++
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0
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