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Fastphylo: Fast tools for phylogenetics

Mehmood Alam Khan17*, Isaac Elias14, Erik Sjölund2, Kristina Nylander3, Roman Valls Guimera2, Richard Schobesberger46, Peter Schmitzberger46, Jens Lagergren1 and Lars Arvestad15*

Author Affiliations

1 KTH Royal Institute of Technology, Science for Life Laboratory, School of Computer Science and Communication, Department of Computational Biology, Solna, Sweden

2 Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden

3 KTH Royal Institute of Technology, School of Computer Science and Communication, Stockholm, Sweden

4 KTH Royal Institute of Technology, Stockholm Bioinformatics Center, School of Computer Science and Communication, Department of Computational Biology, Stockholm, Sweden

5 Department of Numerical Analysis and Computer Science, Swedish e-Science Research Centre (SeRC), Stockholm University, Stockholm, Sweden

6 University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Department of Medical and Bioinformatics, Hagenberg, Austria

7 UET University of Engineering and Technology Peshawar, Department of Computer Science and Information Technology, Peshawar, Pakistan

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BMC Bioinformatics 2013, 14:334  doi:10.1186/1471-2105-14-334

Published: 20 November 2013



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.