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Lambda: the Local Aligner for Massive Biological DatA
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Lambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...
* is highly compatible to BLAST (bit-score 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-conforming ``.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
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| **Executables** |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.disk.download.png | Pre-built executables for GNU/Linux, Mac and FreeBSD are available from the |
| :alt: Download Executables | `releases page <https://github.com/seqan/lambda/releases>`__. |
| :target: https://github.com/seqan/lambda/releases | |
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| **Source code** |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.column.three.png | You can also build lambda from source which will result in binaries optimized for your |
| :alt: Build from source | specific system (and thus faster). For instructions, please see the |
| :target: https://github.com/seqan/lambda/wiki | `wiki <https://github.com/seqan/lambda/wiki>`__. |
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usage instructions
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Before you can search, you need to have an index. You can
1. download and unzip a pre-built index from the `wiki <https://github.com/seqan/lambda/wiki>`__; or
2. index one yourself (this can take some time but only has to be done once):
::
% bin/lambda3 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/lambda3 searchp -q query.fasta -i db.fasta.lba
*(in case you want to perform a nucleotide search, instead use* ``searchn`` *)*
For a list of options, see the help pages:
::
% bin/lambda3 --help
% bin/lambda3 COMMAND --help
Advanced options are available via ``--full-help`` or the man pages, and more documentation is available
in the `wiki <https://github.com/seqan/lambda/wiki>`__.
authorship and copyright
------------------------
Lambda is developed by `Hannes Hauswedell <mailto:h2 (æð) fsfe.org>`__ and `Sara Hetzel <mailto:hetzel (æð) molgen.mpg.de>`__ .
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| **Please always cite the publication, also if using Lambda in comparisons and pipelines** |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.book.hardcover.open.png | *Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences*; |
| :alt: Please cite | Hannes Hauswedell, Sara Hetzel et al.; |
| :target: https://academic.oup.com/bioinformatics/article/40/3/btae097/7629128 | `Bioinformatics 2024 40 (3) <https://academic.oup.com/bioinformatics/article/40/3/btae097/7629128>`__; |
| :width: 76px | doi: 10.1093/bioinformatics/btae097 |
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| **The original Lambda publication (versions before 3)** |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.book.hardcover.open.png | *Lambda: the local aligner for massive biological data*; |
| :alt: Please cite | Hannes Hauswedell, Jochen Singer, Knut Reinert; |
| :target: http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract | `Bioinformatics 2014 30 (17): i349-i355 <http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract>`__; |
| :width: 76px | doi: 10.1093/bioinformatics/btu439 |
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| **Please respect the license of the software** |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/copyleft.png | Lambda is Free and open source software, so you can use it for any purpose, free of charge. |
| :alt: Respect the license | However certain conditions apply when you (re-)distribute and/or modify Lambda, please respect the |
| :target: https://github.com/seqan/lambda/blob/master/LICENSE.rst | `license <https://github.com/seqan/lambda/blob/master/LICENSE.rst>`__. |
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feedback & updates
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.social.github.octocat.png | You can ask questions and report bugs on the `github tracker <https://github.com/seqan/lambda/issues>`__ . |
| :alt: GitHub | Please also `subscribe <https://github.com/seqan/lambda/subscription>`__ and/or star us! |
| :target: https://github.com/seqan/lambda/issues | |
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*icons on this page by Austin Andrews / https://github.com/Templarian/WindowsIcons*