search

soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
GNU General Public License v3.0
1.39k stars 195 forks source link

Support more substitution matrices #20

Closed martin-steinegger closed 7 years ago

martin-steinegger commented 7 years ago

Expected Behavior

It should be possible to change the substitution matrice in MMseqs2.

Current Behavior

Currently MMseqs2 only supports matrices that are defined in BlastScoreUtils. We have to fit lambda, k, alpha, beta. Maybe ALP (https://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/bib/alp_lib_v1_93.html) can help.

martin-steinegger commented 7 years ago

Included ALP https://github.com/soedinglab/MMseqs2/commit/0c394c83af4ebd3defc6802f3a8a908e38177826

martin-steinegger commented 7 years ago

Added the support for matrix exchange https://github.com/soedinglab/MMseqs2/commit/66b713cc24dcacf7adfb2e58d7e8c33b74adaa3c