Bermudez, J. | Search bioRxiv

bioRxiv2019

Inferring phylogenetic trees from mutational distance of transposable elements.

There are many methods for establishing a phylogeny available to researchers. Some of these are based on the mutational distance between ortholog sequences of DNA, and, from these, some are based on the analysis (presence/absence) of transposable elements in specific loci of ortholog sequences. We present a new approach: a method for inferring a phylogeny based on the mutational distance of transposable elements distributed along any segment of DNA. Our method doesnt require previously having ortholog segments of DNA from every organism. The method can be fully automated, not requiring any previous or posterior data analysis nor data preparation.

evolutionary biology↗

bioRxiv2019

SLAST: Simple Local Alignment Search Tool

We present a local alignment search tool not based on the usual strategy of seed and grow often employed for these tools. Instead, we just find regions in the database sequences having a high density of seed matches and then we perform a Smith-Waterman local alignment of the query sequence into these regions. This approach has some advantages for some use cases.

bioinformatics↗