Aligning to distant homologues

[ens-sb]

What would be a recommended setting for a slower but more sensitive alignment to distant homologues?

[lh3]

You may consider:

• -M0 (denser seeds)
• -M0 -k5 (smaller k-mer)

Note that these may only improve sensitivity a little. I need to redesign the seeding algorithm for higher sensitivity.

[ens-sb]

Thanks a lot!