Etool - Online softwares for biologists
At Etool, we work very hard to publish important bioinformatics tools.
Related publications : Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham
Notes : C-Sibelia is now in stable version.
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.
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:
Signal Refinement is A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments.