Online tools

Online Tools

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MrBayes

Phylogenetic reconstruction

 

Bayesian Inference for Phylogeny

Author(s)

J. P. Huelsenbeck, F. Ronquist


Version

3.1.2


Subsections

Phylogenetic reconstruction


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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


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MRtools is a JAVA 1.6 software that is dedicated to the building of binary representation of a collection of phylogenetic trees.
Three binary coding are available: bipartition- (Baum 1992; Ragan 1992; see also Doyle 1992), triplet- (Nelson and Ladiges 1994; Williams and Humphries 2003; Wilkinson et al. 2004), and quartet-based binary matrix representation. Matrix representations are outputed in NEXUS format, with the possibility to include an 'ASSUMPTIONS' block in order to reduce the size of the binary matrix representation, which is often large and redondant when the triplet- and quartet-based binary coding are used (Ranwez et al. 2010). Moreover, as these two last coding induce redondant information for each input tree (Dekker 1986; Wilkinson et al. 2004), MRtools is able to compute the minimum set of binary characters that entail each input tree (e.g. one per internal branch for a fully resolved tree; Steel 1992). Finally, MRtools implements a very fast heuristics to infer a supertree from the so-built binary matrix representation. As each internal branch of a supertree corresponds to a bipartition-based binary character, confidence value is also computed for each internal brach by computing the proportion of binary characters in the matrix representation that are compatible with the bipartition-based binary character induced by the given branch.

Author(s)

Alexis Criscuolo


Version

1


Tags

under development


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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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