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Tools

Tools are in free access Public access or restricted access Registered access

They run on the web, unix or both.

Tools in restricted access can use unpublished data.


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The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. MCL has been applied in a number of different domains, mostly in bioinformatics. ...

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QTL mapping in multicross design
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A system for quickly aligning entire genomes.
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A multiple alignment sequence tool for amino acid or nucleotide sequences using Fast Fourier Transform.
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Whitehead's Genetic mapping tool
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Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence ...

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A multiple alignment program for large genomic sequences
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Discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences
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MetaGPipe is a wrapper of the QIIME framework and FungalITSExtractor tool. It was especially designed to analyze PCR amplicons of fungal ITS regions sequenced with 454 technology. It was then successfully used with Illumina MiSeq reads.MetaGPipe extracts ITS regions from ...

Plant metabolome for genetic resource analysis, mutant and transformant screening and quantitative trait loci determination
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MOSAIK is a reference-guided assembler comprising of four main modular programs:
  •  MosaikBuild
  •  MosaikAligner
  •  MosaikSort
  •  MosaikAssembler.
 MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end ...

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mothur project a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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Detecting tandem repeats in DNA sequences
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Multiple sequence comparison by log-expectation of amino acid or nucleotide sequences
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A tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed.
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Update: 02 Dec 2011
Creation date: 31 May 2011