Lambda: the Local Aligner for Massive Biological DatA
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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 ``.sam`` and ``.bam`` and many compression types
versions
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| Branch / Repository | Description | Versions | Build state |
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| `master <https://github.com/seqan/lambda/tree/master>`__ | stable | ``0.9.* - 1.0.*`` | .. image:: https://travis-ci.org/seqan/lambda.svg?branch=master |
| | (recommended) | | :alt: Travis CI build status |
| | | | :target: https://travis-ci.org/seqan/lambda |
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| `lambda-next <https://github.com/seqan/lambda/tree/lambda-next>`__ | experimental | ``1.9.* - 2.0.*`` | .. image:: https://travis-ci.org/seqan/lambda.svg?branch=lambda-next |
| | | | :alt: Travis CI build status |
| | | | :target: https://travis-ci.org/seqan/lambda |
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| `old repo <https://github.com/h-2/seqan/tree/feature/lambda>`__ | initially | ``0.4.*`` | |
| | published | | |
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authorship and copyright
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Lambda is being developed by `Hannes Hauswedell <mailto:hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]>`__, but it incorporates a lot of work from other members of the `SeqAn project <http://www.seqan.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 | *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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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>`__. If there is an ``_sse4`` package, try that first, |
| :target: https://github.com/seqan/lambda/releases | it will be faster. |
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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/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 <https://github.com/seqan/lambda/wiki>`__.
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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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.email.png | To stay up to date via e-mail, please subscribe to the |
| :alt: Newsletter | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is on average less than one e-mail |
| :target: https://lists.fu-berlin.de/listinfo/lambda-users | per month. |
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| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.social.twitter.png | You can also follow SeqAn on `twitter <https://twitter.com/SeqAnLib>`__ to receive updates on Lambda. |
| :alt: Newsletter | |
| :target: https://twitter.com/SeqAnLib | |
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*icons on this page by Austin Andrews / https://github.com/Templarian/WindowsIcons*