Lambda: the Local Aligner for Massive Biological DatA

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 .sam and .bam and 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)

downloads and installation

Executables
	Pre-built executables for GNU/Linux, Mac and FreeBSD are available from the releases page.
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.

usage instructions

Before you can search, you need to have an index. You can

1. download and unzip a pre-built index from the wiki; or
2. 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.

authorship and copyright

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.

feedback & updates

	You can ask questions and report bugs on the github tracker . Please also subscribe and/or star us!
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