title: Fastphylo: fast tools for phylogenetics.
abstract: 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.
authors.affiliation: KTH Royal Institute of Technology, Science for Life Laboratory, School of Computer Science and Communication, Department of Computational Biology, Solna, Sweden. malagori@kth.se.
authors.forename: Mehmood Alam
authors.initials: MA
authors.lastname: Khan
authors.forename: Isaac
authors.initials: I
authors.lastname: Elias
authors.forename: Erik
authors.initials: E
authors.lastname: Sjölund
authors.forename: Kristina
authors.initials: K
authors.lastname: Nylander
authors.forename: Roman Valls
authors.initials: RV
authors.lastname: Guimera
authors.forename: Richard
authors.initials: R
authors.lastname: Schobesberger
authors.forename: Peter
authors.initials: P
authors.lastname: Schmitzberger
authors.forename: Jens
authors.initials: J
authors.lastname: Lagergren
authors.forename: Lars
authors.initials: L
authors.lastname: Arvestad
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D005075:Biological Evolution; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D007802:Language; D008568:Memory; D005810:Multigene Family; D010802:Phylogeny; D012984:Software