Lambda is a local aligner optimized for many query sequences and searches in protein space. It is...
- highly compatible to BLAST (bitscore and e-value statistics, tab seperated and verbose output formats)
- much faster than BLAST and many other comparable tools
- supports many other input and output formats, including standards-conformant
.samand.bamand many compression types
| Branch / Repository | Description | Versions | Build state |
|---|---|---|---|
| master | stable (recommended) | 0.9.* - 1.0.* |
|
| lambda-next | experimental | 1.9.* - 2.0.* |
|
| old repo | initially published | 0.4.* |
Lambda is being developed by Hannes Hauswedell, but it incorporates a lot of work from other members of the SeqAn project.
| Please always cite the publication, also if using Lambda in comparisons and pipelines | |
|
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 |
| Please respect the license of the software | |
|
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 and/or modify Lambda, please respect the license. |
| Executables | |
|
Pre-built executables for GNU/Linux, Mac and FreeBSD are available from the
releases page. If there is an _sse4 package, try that first,
it will be faster. |
| Source code | |
|
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. |
Before you can search, you need to have an index. You can
- download and unzip a pre-built index from the wiki; or
- index one yourself (this can take some time but only has to be done once):
% bin/lambda_indexer -d db.fasta
After that running Lambda is as simple as
% bin/lambda -q query.fasta -d db.fasta
For a list of options, see the help pages:
% bin/lambda --help % bin/lambda --full-help
Or visit the Tuning-guide in the wiki.
|
You can ask questions and report bugs on the github tracker . Please also subscribe and/or star us! |
|
To stay up to date via e-mail, please subscribe to the newsletter. There is on average less than one e-mail per month. |
|
You can also follow SeqAn on twitter to receive updates on Lambda. |
icons on this page by Austin Andrews / https://github.com/Templarian/WindowsIcons