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Open Access Software

MafFilter: a highly flexible and extensible multiple genome alignment files processor

Julien Y Dutheil12*, Sylvain Gaillard345 and Eva H Stukenbrock6

Author Affiliations

1 Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany

2 Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, Montpellier 34095, France

3 INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Angers F-49045, France

4 Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Angers F-49045, France

5 Université d’Angers, LUNAM Université, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Angers F-49045, France

6 Max Planck Institute for Terrestrial Microbiology, Fungal Biodiversity Group, Marburg, Germany

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BMC Genomics 2014, 15:53  doi:10.1186/1471-2164-15-53

Published: 22 January 2014

Abstract

Background

Sequence alignments are the starting point for most evolutionary and comparative analyses. Full genome sequences can be compared to study patterns of within and between species variation. Genome sequence alignments are complex structures containing information such as coordinates, quality scores and synteny structure, which are stored in Multiple Alignment Format (MAF) files. Processing these alignments therefore involves parsing and manipulating typically large MAF files in an efficient way.

Results

MafFilter is a command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner. It provides an extensive set of tools which can be parametrized and combined by the user via option files. We demonstrate the software’s functionality and performance on several biological examples covering Primate genomics and fungal population genomics. Example analyses involve window-based alignment filtering, feature extractions and various statistics, phylogenetics and population genomics calculations.

Conclusions

MafFilter is a highly efficient and flexible tool to analyse multiple genome alignments. By allowing the user to combine a large set of available methods, as well as designing his/her own, it enables the design of custom data filtering and analysis pipelines for genomic studies. MafFilter is an open source software available at http://bioweb.me/maffilter webcite.