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iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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This version processes a de novo assembly to generate a fasta reference file and a gtf file.

iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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LS TEST

Tool

 

This is a simple test of Pise

Author(s)

Julien V, Jimmy L


Version

1


Subsections

Tool


Tags

Apps


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MACSE

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 0.9b1

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

0.9b1


Subsections

Alignment


MACSE V1

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 1.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

1.01b


Subsections

Alignment


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MAFFT

Alignment

 

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of

Author(s)

Kazutaka Katoh


Version

6.814b


Subsections

Alignment


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Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Author(s)

Unknown


Version

1.1


Subsections

Tool - Blast


Tags

RNA-seq - Apps


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Used in order to perform a Mantel test based on two distance matrix. The number of permutations can be specified. An HTML file containing a graphical representation of the statistic Z distribution is generated.

Author(s)

Sara Jaillet & Khalid Belkhir


Version

1


Subsections

Tool


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Megablast

Alignment

 

Mega BLAST uses a greedy algorithm [1] for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm.

Author(s)

NCBI -Tao Tao


Version

1


Subsections

Alignment - Blast


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Build database giving a sequence file in order to blast query sequences on it using magablast. Treatment performed using formatDB and megablast (8 cores).

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]


Version

1


Subsections

Blast


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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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