SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences.

Abstract

Background: The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies- a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. SANS is an alignment-free, whole-genome based approach for phylogeny estimation.

Results: Here we present a new implementation SANS ambages with a significantly increased application spectrum. It offers additional types of input data, parallelized processing, and bootstrapping. The source code (C++), documentation, and example data are freely available for download at: https://github.com/gi-bielefeld/sans . SANS can also be launched via the web-interface of the CloWM platform- free of charge, with a standard Life Science account: https://clowm.bi.denbi.de/workflows/0194b78f-9696-7402-a2b8-858508733618/ .

Conclusions: The new version not only shortens processing time on large datasets immensely by parallelization. Being able to also process amino acid sequences and offering a filter for low-abundant DNA read segments also enables new application cases. Bootstrapping and integrated visualization ease and enrich the interpretation of the resulting phylogenies.