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SUNDAJOY

Phylogenetic reconstruction

 

Analyse phylogenetic signals of genes vs. a supermatrix. ...

Author(s)

Celine Scornavacca, Khalid Belkhir and Frederic Delsuc


Version

0.0.1


Subsections

Phylogenetic reconstruction


Tags

Bio++


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SuperTriplets is a triplet-based supertree approach to phylogenomics. It infers supertrees with branch support values.

Author(s)

Ranwez V., Criscuolo A., Douzery E. J. P.


Version

1


TopHat

Mapping

 

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Author(s)

CBCB


Version

1.3.0


Subsections

Mapping


Tags

RNA-seq


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Multiple alignment of protein-coding DNA sequences : Facilitates the multiple alignment of protein-coding DNA sequences by aligning the amino acids sequences they specify.

Author(s)

Bininda-Emonds


Version

1


Subsections

Tool - Alignment


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VCFanlyser

Mapping

 

This tool is aimed at helping to analyse a small to medium vcf files of genotyped individuals from one or more populations.
Descriptive statistics (Pi, MAF spectrum, F, IBS …) , multivariate analysis (PCA and t-SNE) and population structuration (Fst and fastStructure) can be calculated after filtering snps for min MAF and max missing values.

Author(s)

BELKHIR


Version

1


Subsections

Mapping


Velvet

Assembler

 

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Author(s)

Daniel Zerbino and Ewan Birney


Version

0.7


Subsections

Assembler


Tags

De novo


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