Etool - Online softwares for biologists

At Etool, we work very hard to publish important bioinformatics tools.

If you want to be added to this list, please send an e-mail to support@etool.me or contact us.

Sibelia

Related publications : Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham

    

Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species.

It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.

C-Sibelia

Notes : C-Sibelia is now in stable version.

    

C-Sibelia -- This tool is designed for comparison between two genomes represented either in finished form or as sets of contigs. It is able to detect SNPs/SNVs and indels of different scales.

C-Siblia outputs a VCF file describing all found variants, a circos picture describing the rearrangement scenario. C-Sibelia also uses snpEff to annotate the found variants.

BFB

Breakage-fusion-bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids.

When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions where duplicated segments are arranged head-to-head.

This software (BFB) facilitates the analysis of BFB mechanism in genomes.

SFselect

Selective sweeps leave a detectable signature on the site frequency spectrum. The specific signature, however, depends (among other things) on the time since the sweep begun (t), and on the strength of selection (s). In addition, the demographic history of a population also affects the site frequency spectrum.

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally. We consider a "hard sweep" model of natural selection, where a single (novel) beneficial allele sweeps through the population. Our method is based on a form of supervised learning (Support Vector Machines), where the features for learning and classification are given by the scaled Site Frequency Spectrum in a region.

SFselect can be used in different ways:

  • Classify polymorphism data using a pre-trained general model that is robust to many different combinations of (s,t) values, while maintaining high power. Barring reliable knowledge of the selective sweep, we recommend using this option.
  • Classify polymorphism data using a pre-trained specific model that is most powerful for a given combination of (s,t) values. These specific models do not generalize as well for other (s,t) values. This option may be used given reliable knowledge of the selective sweep.
  • Classify polymorphism data using your own trained model. This option may be used given reliable knowledge of the demographic history. Please contact me (see below) for assistance if you wish to do this.

Signal Refinement

Signal Refinement is A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments.