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fastphylo :
fastphylo : Fast tools for phylogenetics
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- Khan, Mehmood Alam (författare)
- KTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab
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- Elias, Isaac (författare)
- KTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab
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- Sjölund, Erik (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),DBB
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- Nylander, Kristina (författare)
- KTH,Skolan för datavetenskap och kommunikation (CSC)
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- Guimera, Roman Valls (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholms univetsitet
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- Schobesberger, Richard (författare)
- KTH,Beräkningsbiologi, CB,University of Applied Sciences Upper Austria
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- Schmitzberger, Peter (författare)
- KTH,Beräkningsbiologi, CB,University of Applied Sciences Upper Austria
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- Lagergren, Jens (författare)
- KTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab
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- Arvestad, Lars (författare)
- Stockholms universitet,KTH,Beräkningsbiologi, CB,Science for Life Laboratory, SciLifeLab,Numerisk analys och datalogi (NADA)
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(creator_code:org_t)
- 2013-11-20
- 2013
- Engelska.
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Ingår i: BMC Bioinformatics. - : BioMed Central. - 1471-2105. ; 14:1, s. 334-
- Relaterad länk:
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http://www.biomedcen...
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https://kth.diva-por... (primary) (Raw object)
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https://bmcbioinform...
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https://doi.org/10.1...
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https://su.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Distance matrices
- Distance method
- Evolutionary history
- Large problems
- Memory efficient
- Modular architectures
- Neighbor joining
- Phylogenetic studies
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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