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 separated and verbose output formats)
- is much faster than BLAST and many other comparable tools
- supports many other input and output formats, including standards-conformant
.samand.bamand many compression types - has special features for species annotation and taxonomic analysis
- is well-documented and easy to use (e.g. provides progress-bars and memory usage estimates)
| Executables | |
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Pre-built executables for GNU/Linux, Mac and FreeBSD are available from the releases page. |
| Source code | |
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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/lambda2 mkindexp -d db.fasta
(in case you want to create a nucleotide index, instead use ``mkindexn``)
After that running Lambda is as simple as
% bin/lambda2 searchp -q query.fasta -i db.fasta.lambda
(in case you want to perform a nucleotide search, instead use ``searchn``)
For a list of options, see the help pages:
% bin/lambda2 --help % bin/lambda2 COMMAND --help
Advanced options are available via --full-help or the man pages, and more documentation is available
in the wiki.
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 | |
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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 | |
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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. |
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You can ask questions and report bugs on the github tracker . Please also subscribe and/or star us! |
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To stay up to date via e-mail, please subscribe to the newsletter. There is on average less than one e-mail per month. |
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You can also follow SeqAn on twitter to receive updates on Lambda. |
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