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DNAbushmeat

database

 

DNA-typing of African forest bushmeat.

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game —mostly mammals— per year. Because the bushmeat items sold on markets may consist of unrecognizable pieces of processed meat, we provide a species-identification genetic tool based on ‘forensically informative nucleotide sequencing’ (FINS) to complement standard bushmeat surveys. Our expert-curated nucleotide datasets shall be progressively fed to become a reference frame for the DNA-typing of African forest bushmeat.

Author(s)

Julien VEYSSIER, Remy DERNAT, Khalid Belkhir and Philippe GAUBERT


Version

1.1


Subsections

database


Tool to upload new database versions into DNAbushmeat.

Author(s)

Unknown


Version

1


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DNAdist

Phylogenetic reconstruction

 

Compute distance matrix from nucleotide sequences

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


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Online tool for ecceTERA

Author(s)

Edwin Jacox, Celine Scornavacca, Julien Veyssier


Version

1


Edena

Assembler

 

Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. All exact overlaps between any pair of reads are computed and structured in a graph (overlap step). Basically, the reads are indexed in a prefix array and overlaps are revealed by dichotomic search in the arrays. The graph is then analyzed to remove transitive and spurious edges (layout step). Finally, contigs that can be assembled following unambiguous path in the graph are given as output. Edena allows to produce contigs of several kbp with a near full coverage of the bacterial genome being sequenced.

Author(s)

D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel


Version

2.1.1


Subsections

Assembler


Tags

De novo


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Translate Illumina Bustard output to a fastq file

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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Euler

Assembler

 

EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.

Author(s)

Mark Chaisson, Pavel Pevzner, Dumitru Brinza, Haixu Tang, Glenn Tesler


Version

1.1.2


Subsections

Assembler


Tags

De novo


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A little test for Auto_Pise .

Author(s)

Unknown


Version

1


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Garli

Phylogenetic reconstruction

 

Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

Author(s)

Derrick J. Zwickl


Version

0.96


Subsections

Phylogenetic reconstruction


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Gblocks

Alignment

 

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Author(s)

Jose Castresana


Version

1


Subsections

Alignment


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Genepop implements a mixture of traditional methods and some more focused developments: It computes exact tests for Hardy-Weinberg equilibrium, for population erentiation and for genotypic disequilibrium among pairs of loci; It computes estimates of F-statistics, null allele frequencies, allele size- based statistics for microsatellites, etc., and of number of immigrants by Barton and Slatkin s 1986 private allele method; It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including condence intervals for neighborhood size.

Author(s)

François Rousset


Version

4.0


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IDxen

Pipeline

 

IDxen : EPA on mitochondrial reads.

Author(s)

Julien Veyssier


Version

1


Subsections

Pipeline - Tool


IDxen upload

Alignment

 

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier


Version

1


Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool


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IM program for fitting the Isolation w/ Migration model using a MCMC method : IM is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

1


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IMa program for fitting the Isolation w/ Migration model using a MCMC method : IMa is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

2.0


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