Lambda is a local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Please cite the following if you use Lambda anywhere in your academic work, also as part of pipelines or comparisons:
Lambda: the local aligner for massive biological data; Hannes Hauswedell, Jochen Singer, Knut Reinert; Bioinformatics 2014 30 (17): i349-i355; doi: 10.1093/bioinformatics/btu439
The latest version is available here. Versions prior to 0.9.0 are available here.
Lambda is Free and open source software, so you can use it for any purpose, free of charge. However certain conditions apply when you (re-)distribute or modify Lambda, please respect the license.
You can also build lambda from source which will result in binaries optimized for your specific system (and thus faster). For instructions, please see the wiki.
Optionally mask the database:
% /path/to/segmasker -infmt fasta -in db.fasta -outfmt interval -out db.seg
Run the indexer (or check the wiki for pre-built indexes!):
% bin/lambda_indexer -d db.fasta [-s db.seg]
Run lambda:
% bin/lambda -q query.fasta -d db.fasta
Please note that if you downloaded the binaries from the web-site, you might also have bin/lambda-avx which is
measurably faster, so try that first!
For a list of options, see the help pages:
% bin/lambda --help % bin/lambda --full-help
Or visit the Tuning-guide in the wiki.
Please report bugs to the bug-tracker.
Any other questions or feedback you can send to Hannes Hauswedell.
Thank you for using Lambda, we hope that it is useful to you!