Åpne denne publikasjonen i ny fane eller vindu >>Vise andre…
2013 (engelsk)Inngår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 14, nr 1, s. 334-Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]
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.
sted, utgiver, år, opplag, sider
BioMed Central, 2013
Emneord
Distance matrices, Distance method, Evolutionary history, Large problems, Memory efficient, Modular architectures, Neighbor joining, Phylogenetic studies
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-136421 (URN)10.1186/1471-2105-14-334 (DOI)000329901900001 ()24255987 (PubMedID)2-s2.0-84887664660 (Scopus ID)
Forskningsfinansiär
Swedish e‐Science Research CenterScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Merknad
QC 20140205
2013-12-052013-12-052024-03-15bibliografisk kontrollert