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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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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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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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wgsim simulator program from samtools

Author(s)

Heng Li


Version

1


Subsections

Tool - Mapping


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Base composition and read size distribution

Author(s)

MBB dev team


Version

1


Subsections

Tool


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ReadSeq

Tool

 

Readseq was written originally around 1989 a component of a sequence analysis program, but when I added a small, simple command-line interface, it took on a life of its own as a conversion program for bioinformatics. It's main contribution to bioinformatics is it takes on the job of guessing what your input biosequence data format is, and converting it to what your software knows how to handle.

Author(s)

D. Gilbert


Version

1


Subsections

Tool


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Under development

Author(s)

MBB Development team


Version

1


Subsections

Tool


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