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  andi: fast and accurate estimation of evolutionary distances between closely related genomes

Haubold, B., Klötzl, F., & Pfaffelhuber, P. (2015). andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics, 31(8), 1169-1175. doi:10.1093/bioinformatics/btu815.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0024-9D24-0 Version Permalink: https://hdl.handle.net/21.11116/0000-0005-1A13-9
Genre: Journal Article

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Haubold_Kloetzl Pfaffelhuber_2014.pdf (Publisher version), 4MB
 
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 Creators:
Haubold, Bernhard1, Author           
Klötzl, Fabian1, Author           
Pfaffelhuber, Peter, Author
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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 Abstract: Motivation: A standard approach to classifying sets of genomes is to calculate their pairwise
distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly
computing the evolutionary distances between closely related genomes.
Results: Our distance measure is based on ungapped local alignments that we anchor through
pairs of maximal unique matches of a minimum length. These exact matches can be looked up
efficiently using enhanced suffix arrays and our implementation requires approximately only 1 s
and 45 MB RAM/Mbase analysed. The pairing of matches distinguishes non-homologous from
homologous regions leading to accurate distance estimation. We show this by analysing simulated
data and genome samples ranging from 29 Escherichia coli/Shigella genomes to 3085 genomes of
Streptococcus pneumoniae.
Availability and implementation: We have implemented the computation of anchor distances
in the multithreaded UNIX command-line program andi for ANchor DIstances. C sources and
documentation are posted at http://github.com/evolbioinf/andi/
Contact: haubold@evolbio.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.

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Language(s): eng - English
 Dates: 2014-11-062014-07-012014-12-072014-12-102015-04-15
 Publication Status: Issued
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 Table of Contents: -
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 Identifiers: DOI: 10.1093/bioinformatics/btu815
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 31 (8) Sequence Number: - Start / End Page: 1169 - 1175 Identifier: ISSN: 1367-4803 (print)
ISSN: 1460-2059 (online)
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991