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Fastphylo: Fast tools for phylogenetics
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 14, 334- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Distance methods are ubiquitous tools in phylogenetics.Their primary purpose may be to reconstructevolutionary history, but they are also used as components in bioinformatic pipelines. However, poorcomputational efficiency has been a constraint on the applicability of distance methods on very largeproblem instances.

RESULTS: We present fastphylo, a software package containing implementations of efficient algorithms for twocommon problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing aphylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methodsand 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
2013. Vol. 14, 334- p.
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:su:diva-97257DOI: 10.1186/1471-2105-14-334ISI: 000329901900001PubMedID: 24255987OAI: diva2:676302
Swedish e‐Science Research CenterScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2013-12-05 Created: 2013-12-05 Last updated: 2014-02-10Bibliographically approved

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Sjölund, ErikGuimera, Roman VallsArvestad, Lars
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Department of Biochemistry and BiophysicsScience for Life Laboratory (SciLifeLab)Numerical Analysis and Computer Science (NADA)
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