Recco is a free program that 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.

NOTE: Recco is free for non-commercial use.

Requirements:

· Java 1.5 or later

What's New in This Release: [ read full changelog ]

· several minor bugs fixed (involving GUI repainting, command line processing among others)
· "View => Optimal Solution Only" shows the optimal solutions only
· "Opt Seqsel" button removes sequences from the alignment such that evidence for recombination for the currently selected sequence is maximized
· command line changed: more options, slightly different syntax, command line description now correct.
· selection of an amino-acid model from the menu now works