Fastphylo: fast tools for phylogenetics

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 lar...

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Bibliographic Details
Published in:BMC bioinformatics 2013-11, Vol.14 (1), p.334-334, Article 334
Main Authors: Khan, Mehmood Alam, Elias, Isaac, Sjölund, Erik, Nylander, Kristina, Guimera, Roman Valls, Schobesberger, Richard, Schmitzberger, Peter, Lagergren, Jens, Arvestad, Lars
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Analysis
Biological Evolution
Computational Biology - instrumentation
Computational Biology - methods
Computer programs
Distance matrices
Distance method
Evolutionary history
Genomics
Language
Large problems
Memory
Memory efficient
Modular architectures
Multigene Family
Neighbor joining
Phylogenetic studies
Phylogenetics
Phylogeny
Science
Software
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Summary: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. 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. 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.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-14-334