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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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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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MBB version of SeqClean (used to remove adaptators)

Author(s)

The Institute for Genomic Research - Geo Pertea


Version

1


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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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Soap2

Mapping

 

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Author(s)

T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu


Version

2.20


Subsections

Mapping


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The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

Author(s)

Pritchard, Stephens, Donnelly, Hubisz, Falush


Version

2.3.4


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This tool use the same version as structure but it needs parameters files.

Author(s)

Pritchard, Stephens, Donnelly, Falush and Hubisz (code only)


Version

2.3.4


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