Online tools

Results

Query : Phylogenetic reconstruction [subsection]

Online Tools (11)

DNAdist

Phylogenetic reconstruction

 

Compute distance matrix from nucleotide sequences

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


Garli

Phylogenetic reconstruction

 

Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

Author(s)

Derrick J. Zwickl


Version

0.96


Subsections

Phylogenetic reconstruction


MrBayes MCMC convergence plotter

Phylogenetic reconstruction

 

A visual tool to diagnose the convergenge of MrBayes MCMCM

Author(s)

Khalid Belkhir


Version

1


Subsections

Phylogenetic reconstruction


Neighbor

Phylogenetic reconstruction

 

Neighbor-Joining and UPGMA methods

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


PhyML

Phylogenetic reconstruction

 

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

Author(s)

S. Guindon and O. Gascuel


Version

3.0


Subsections

Phylogenetic reconstruction


RAxML-VI-HPC

Phylogenetic reconstruction

 

Phylogenetic tree inference using maximum likelihood/rapid bootstrapping. On this portal, the baseModel is forced as GTRGAMMA for dna and PROTGAMMA for protein

Author(s)

Alexandros Stamatakis


Version

1


Subsections

Phylogenetic reconstruction


PAUP

Phylogenetic reconstruction

 

PAUP is the most widely used package for phylogenetic inference, and now implements

Author(s)

swofford


Version

4


Subsections

Phylogenetic reconstruction


Tags

under development


1 -> Alignment (ClustalW / Mafft / Muscle)
2 -> Gblocks
3 -> Phylogenetic reconstruction (Phyml / RaxML HPC MPI / MrBayes)
Under developement

Author(s)

MBB development Team


Version

0.0


Subsections

Pipeline - Phylogenetic reconstruction - Alignment


MrBayes

Phylogenetic reconstruction

 

Bayesian Inference for Phylogeny

Author(s)

J. P. Huelsenbeck, F. Ronquist


Version

3.1.2


Subsections

Phylogenetic reconstruction


SUNDAJOY

Phylogenetic reconstruction

 

Analyse phylogenetic signals of genes vs. a supermatrix. ...

Author(s)

Celine Scornavacca, Khalid Belkhir and Frederic Delsuc


Version

0.0.1


Subsections

Phylogenetic reconstruction


Tags

Bio++


IDxen upload

Alignment

 

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier


Version

1


Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool


Softwares (2)

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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Documents (5)

Formation Introduction à la phylogénétique et la génomique avec R

Phylogenetic reconstruction

 

Documents et liens relatifs à la formation "Introduction à la phylogénétique et la génomique avec R" organisée par Mbb du 26 au 28 mars 2014 à Montpellier. La partie adGenet de Thibaut Jombart est disponible : http://adegenet.r-forge.r-project.org/documentation.html .
Les diapos de l'intervention d'Emmanuel Paradis sont à télécharger ici.

Author(s)

Emmanuel Paradis


Downloads

0


Subsection

Phylogenetic reconstruction




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