Online tools

Online Tools

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Description to write

Author(s)

Julien Veyssier and Nicolas Barthes


Version

1


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This OnlineTool is a wrapper for structure software http://pritch.bsd.uchicago.edu/structure.html

It is the same wrapper as structure_param, however, you can specify a maximum and a minimum value for K (structure_param is an OnlineTool for structure but you have to give extraparam and mainparam file).

Author(s)

Pritchard, Stephens, Donnely, Falush, Hubisz


Version

2.3.4


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Neighbor

Phylogenetic reconstruction

 

Neighbor-Joining and UPGMA methods

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


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OMM_MACSE

Pipeline

 

Align coding sequences using MACSE (OrthoMaM pipeline)

Author(s)

Vincent Ranwez


Version

0.2.0


Subsections

Pipeline - Alignment


Tags

Apps


PASS

Mapping

 

PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by Solexa, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming. Pass is useful for single read mapping, paired-end resequensing, small RNA discovery and RNA-seq mapping.

Author(s)

Campagna et al


Version

1.2


Subsections

Mapping


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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


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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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First cfit online tool

Author(s)

Unknown


Version

1


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Program to compute distance matrix from protein sequences

Author(s)

Felsenstein


Version

3.67


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RADrefMap

Mapping

 

Test RAD on reference genome

Author(s)

Unknown


Version

1


Subsections

Mapping


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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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Reciprocal Best Hit

Author(s)

Wrapper by MBB Development team


Version

1


Subsections

Blast


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