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.

ADseq – Comparative Scaffolding

ADseq

:: DESCRIPTION

ADseq is a new method, that allows to improve scaffolding of extant genomes and jointly reconstructs gene order in ancestral genomes.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ADseq

:: MORE INFORMATION

Citation

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S.
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
BMC Genomics. 2018 May 9;19(Suppl 2):96. doi: 10.1186/s12864-018-4466-7. PMID: 29764366; PMCID: PMC5954271.

DeClone – Evolutionary Scenarios for Gene Adjacencies in a Gibbs-Boltzmann framework

DeClone

:: DESCRIPTION

DeClone is a software for the prediction of ancestral adjacencies in reconciled gene trees.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

DeClone

:: MORE INFORMATION

Citation

Chauve C, Ponty Y, Zanetti J.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
BMC Bioinformatics. 2015;16 Suppl 19(Suppl 19):S6. doi: 10.1186/1471-2105-16-S19-S6. Epub 2015 Dec 16. PMID: 26696141; PMCID: PMC4686788.

DeCoStar – Reconstructing Parsimonious histories of Gene Adjacencies

DeCoStar

:: DESCRIPTION

DeCoSTAR is a program designed to study the evolution of links between genes (i.e., adjacencies) .

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

DeCoStar

:: MORE INFORMATION

Citation

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E.
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.
Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069. PMID: 28402423; PMCID: PMC5441342.

FPSAC 1.0 – Comparative Scaffolding of Ancient Contigs.

FPSAC 1.0

:: DESCRIPTION

FPSAC (Fast Phylogentic Scaffolding of Ancient Contigs) is a software for fast phylogenetic scaffolding of ancient contigs. The author apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python

:: DOWNLOAD

FPSAC

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24.
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Rajaraman A, Tannier E, Chauve C.

phylostan – Phylogenetic Inference using Stan

phylostan

:: DESCRIPTION

phylostan is a tool written in python for inferring phylogenetic trees from nucleotide datasets. It generates a variety of phylogenetic models using the Stan language.

::DEVELOPER

Mathieu Fourment

SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

phylostan

:: MORE INFORMATION

STS v0.1 – Sequential Tree Sampler for online Phylogenetics

STS v0.1

:: DESCRIPTION

STS implements a prototype of online phylogenetics, updating a posterior distribution generated by MrBayes with new sequences.

::DEVELOPER

Mathieu Fourment

SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

STS

:: MORE INFORMATION

Citation

Claywell BC, Dinh V, Fourment M, McCoy CO, Matsen Iv FA.
A Surrogate Function for One-Dimensional Phylogenetic Likelihoods.
Mol Biol Evol. 2018 Jan 1;35(1):242-246. doi: 10.1093/molbev/msx253. PMID: 29029199; PMCID: PMC5850616.

physher v1.0.2 – Phylogenetic Analysis of Genetic data

physher v1.0.2

:: DESCRIPTION

Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic data.

::DEVELOPER

Mathieu Fourment

SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Physher

:: MORE INFORMATION

Citation

Fourment M, Holmes EC.
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.
BMC Evol Biol. 2014 Jul 24;14:163. doi: 10.1186/s12862-014-0163-6. PMID: 25055743; PMCID: PMC4222489.

CAT/BAT v5.2.3 – Taxonomic Classification of Contigs and Metagenome-assembled Genomes

CAT/BAT v5.2.3

:: DESCRIPTION

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

::DEVELOPER

Bas E. Dutilh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

CAT/BAT

:: MORE INFORMATION

Citation

von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.
Genome Biol. 2019 Oct 22;20(1):217. doi: 10.1186/s13059-019-1817-x. PMID: 31640809; PMCID: PMC6805573.

Patristic – Input different Tree files and computes their Patristic Distances

Patristic

:: DESCRIPTION

Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances.

::DEVELOPER

Mathieu Fourment

SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

Patristic

:: MORE INFORMATION

Citation

Fourment M, Gibbs MJ.
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change.
BMC Evol BIOl. 2006; 6:1