Fastphylo: Fast tools for phylogenetics

Mehmood Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
2013 BMC Bioinformatics  
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
more » ... tances 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. Implementation Fastphylo consists of four modules: fastdist, fastprot, fastprot_mpi, and fnj. All these modules are implemented in C++ (compiled with GCC v4.7) and have been verified to compile on popular
doi:10.1186/1471-2105-14-334 pmid:24255987 pmcid:PMC4225504 fatcat:47xbjep3anbm3nrnusse2quasm