Max-Planck-Institut für Informatik
max planck institut
mpii logo Minerva of the Max Planck Society

Recco - Recombination Analysis Using Cost Optimization

Recco analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence with all other sequences in the alignment using mutation and recombination. A parametric analysis of the parameter alpha, which weights recombination cost against mutation cost, yields additional information as to which sequence might be recombinant.

Screenshots are on the Walkthrough page. For more details, please refer to the publication stated below.



The handling of gaps in version 0.91 of Recco results in wrong p-values for recombination if gap opening costs are non-zero! Please do not use gap open costs! Also, there is a publication using Recco to analyze a very difficult dataset with large gap regions. The supplement describes a heuristic way to cope with gaps, but you may also contact me (Jochen Maydt) directly.

Version 0.93, release date: September 25th, 2007

New Walkthrough Guide - it summarizes my experience using Recco and talks about the do's and dont's! The manual was also updated.

New features:

Version 0.92, release date: September 6th, 2006

New features:


Version 0.91, release date: July 17th, 2006

New features:


Version 0.9, release date: May 23rd, 2006

New features:

Missing features and known bugs:


Version 0.1, release date: February 6th, 2006

This is a preliminary version. It still misses many features discussed in the accompanying paper: it can only handle nucleotide sequence, it does not compute permutation tests so far and has no printing facility built-in. An updated version is in progress.


Please cite Recco as follows:
Maydt, J. and T. Lengauer (2006). "Recco: Recombination Analysis Using Cost Optimization.", Bioinformatics 2006, 22(9):1064-1071, doi:10.1093/bioinformatics/btl057. [PDF] [Abstract]. The links to the full-text article are kindly provided by Oxford University Press.

A case study was published in Retrovirology:
Flockerzi A., Maydt J., Frank O., Ruggieri A., Maldener E., Seifarth W., Medstrand P., Lengauer T., Meyerhans A., Leib-Mosch C., Meese E. and J. Mayer. "Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.", Retrovirology, June 2007, [Full-Text].


If you have questions, comments, criticism etc. do not hesitate to contact me, Jochen Maydt.