andi

The software tool 'andi' provides a fast and accurate algorithm for computing evolutionary distances between closely related genomes. The algorithm is based on ungapped local alignments anchored through pairs of maximal unique matches, which distinguish non-homologous from homologous regions. The implementation requires only 1 s and 45 MB RAM/Mbase analyzed, and has been validated on simulated data and genome samples ranging from 29 to 3085 genomes. The 'andi' tool is available as a multithreaded UNIX command-line program, with C sources and documentation provided.

Topic

Phylogenetics

Detail

  • Operation: Sequence distance matrix generation

  • Software interface: Command-line user interface

  • Language: C

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: v0.14

  • Credit: Deutsche Forschungsgemeinschaft

  • Input: FASTA

  • Output: -

  • Contact: kloetzl@evolbio.mpg.de;kloetzl@evolbio.mpg.de

  • Collection: -

  • Maturity: -

Publications

  • andi: fast and accurate estimation of evolutionary distances between closely related genomes.
  • Haubold B, et al. andi: fast and accurate estimation of evolutionary distances between closely related genomes. andi: fast and accurate estimation of evolutionary distances between closely related genomes. 2015; 31:1169-75. doi: 10.1093/bioinformatics/btu815
  • https://doi.org/10.1093/bioinformatics/btu815
  • PMID: 25504847
  • PMC: -

Download and documentation

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