Fastphylo [Elektronisk resurs] Fast tools for phylogenetics

• 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. 

Ämnesord

Natural Sciences  (hsv)

Computer and Information Science  (hsv)

Bioinformatics (Computational Biology)  (hsv)

Naturvetenskap  (hsv)

Data- och informationsvetenskap  (hsv)

Bioinformatik (beräkningsbiologi)  (hsv)