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  • Khan, Mehmood AlamKTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab (author)

fastphylo : Fast tools for phylogenetics

  • Article/chapterEnglish2013

Publisher, publication year, extent ...

  • 2013-11-20
  • BioMed Central,2013
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:kth-136421
  • https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-136421URI
  • https://doi.org/10.1186/1471-2105-14-334DOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-97257URI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • QC 20140205
  • 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Elias, IsaacKTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1omod4k (author)
  • Sjölund, ErikStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),DBB(Swepub:su)ersj (author)
  • Nylander, KristinaKTH,Skolan för datavetenskap och kommunikation (CSC)(Swepub:kth)u1tkxiyi (author)
  • Guimera, Roman VallsStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholms univetsitet(Swepub:su)rvall (author)
  • Schobesberger, RichardKTH,Beräkningsbiologi, CB,University of Applied Sciences Upper Austria(Swepub:kth)u1iz3phi (author)
  • Schmitzberger, PeterKTH,Beräkningsbiologi, CB,University of Applied Sciences Upper Austria(Swepub:kth)u1uage9b (author)
  • Lagergren, JensKTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab(Swepub:kth)u13fcyg9 (author)
  • Arvestad, LarsStockholms universitet,KTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab,Numerisk analys och datalogi (NADA)(Swepub:su)arve (author)
  • KTHBeräkningsbiologi, CB (creator_code:org_t)

Related titles

  • In:BMC Bioinformatics: BioMed Central14:1, s. 334-1471-2105

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