fastphylo : Fast tools for phylogenetics

• 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

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