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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Tools in restricted access can use unpublished data.


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Fast and Accurate Spliced Alignments of Sequence Reads
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The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs (Hoede C. et al. 2014). It browses the whole spectrum of ...

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Whole genome alignment software
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Computer science resources
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Sequence converter: format phred file in fasta format
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sequence assembly for phred files
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Sequence chromatogram base caller (ABI or SCF format)
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PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been ...

Phylogeny suite:
  • dnadist : DNA sequences (unix command dnadist)
  • dnapars : DNA sequences (unix command dnapars)
  • drawgram : Tree, plotting, consensus (unix command drawgram)
  • drawtree :Tree, plotting, consensus (unix command ...

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PHYTOPROT consists in performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences (Mohseni-Zadeh et al., Recomb 2003) based on their similarity and finally displaying à la Prodom the domains shared by the sequences ...

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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM ...

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Genomic repeat analysis software
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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Multiple alignment sequence
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PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to ...

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SNPs and indels detection pipeline.
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Prediction: distinguish between mitochondrial and plastid targeting sequences
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Sequence primer searching
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Sequence primer searching and designing PCR primers
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Prot4EST is a computer program that takes expressed sequence tags (ESTs) and translates them to produce putative peptides.
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Prediction of protein subcellular localization sites from their amino acid sequences for plant.
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Prediction of protein subcellular localization sites from their amino acid sequences, for yeast and animals
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PyroBayes is a base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequencesMore information is available on Marth Lab Web page.
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Update: 02 Dec 2011
Creation date: 31 May 2011