Online tools Phylogenomics

Online Tools

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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


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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


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Popphyl pipeline

Author(s)

MBB developpers


Version

1


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Program to compute distance matrix from protein sequences

Author(s)

Felsenstein


Version

3.67


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This pipeline implements a RADseq analysis workflow based on the denovo approach of Stacks software.

Author(s)

M. Massaviol & K. Belkhir


Version

1


A reference mapping pipeline using Stacks software.

Author(s)

M. Massaviol & K. Belkhir


Version

1


RADsim

Alignment

 

This interactive application is an R shiny wrapper around the SIMRAD package. Given a particular genome, the user can simulate an inSillico RAD sequencing experiment. Interactively playing with different parameters including fragments size and Restriction enzymes one can assess the amount of sequencing runs needed for a multiplexing design and an expected coverage.

Author(s)

BELKHIR


Version

1


Subsections

Alignment - Mapping - Tool


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


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RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post- analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

Version 8 manual can be found here.

Author(s)

Alexandros Stamatakis


Version

8.0.23


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This tool is a wrapper around NCBI blast.
It allows users to blast their sequences on NCBI nr database or on a their own database that will be cretaed from an uploded fasta file.

Author(s)

BELKHIR


Version

1


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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++


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SuperTriplets is a triplet-based supertree approach to phylogenomics. It infers supertrees with branch support values.

Author(s)

Ranwez V., Criscuolo A., Douzery E. J. P.


Version

1


Multiple alignment of protein-coding DNA sequences : Facilitates the multiple alignment of protein-coding DNA sequences by aligning the amino acids sequences they specify.

Author(s)

Bininda-Emonds


Version

1


Subsections

Tool - Alignment


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