Example Scripts

[Robert Fitak]

Dear MafFilter users,
I have been working with MafFilter for a couple months now, and find it a rather fast and powerful approach for producing basic statistics from genome alignments.  I also hope MafFilter will expand in the future to include additional parameters.  Just for the sake of helping others, I have attached some example scripts of mine that have worked successfully.  The input was an alignment, made using MUGSY, of two ~2GB sized mammalian genome.  Hopefully they provide a good starting point for others.
Bob

[Julien Yann Dutheil]

Dear Robert,

Thanks a lot for these examples. Feedback is always welcome. We are extending MafFilter, mostly based on our own needs in the lab, and also according to user requests (when that is feasible). Note that MafFilter is based on the bpp-seq-omics library, which contains interfaces for creating one's own filters. With a bit of C++ programming, it is actually not too difficult to implement dedicated tools.

All the best,

Julien.