fastphylo: Fast tools for phylogenetics
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 14, no 1, 334- p.Article in journal (Refereed) Published
Background: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances. Results: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency. Conclusions: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.
Place, publisher, year, edition, pages
BioMed Central, 2013. Vol. 14, no 1, 334- p.
Distance matrices, Distance method, Evolutionary history, Large problems, Memory efficient, Modular architectures, Neighbor joining, Phylogenetic studies
Bioinformatics (Computational Biology)
IdentifiersURN: urn:nbn:se:kth:diva-136421DOI: 10.1186/1471-2105-14-334ISI: 000329901900001PubMedID: 24255987ScopusID: 2-s2.0-84887664660OAI: oai:DiVA.org:kth-136421DiVA: diva2:676061
FunderSwedish e‐Science Research CenterScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
QC 201402052013-12-052013-12-052016-10-10Bibliographically approved