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[doc] prep for release
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‎INFO

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Name: lambda
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Author: Hannes Hauswedell <[email protected]>
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Maintainer: Hannes Hauswedell <[email protected]>
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Author: Hannes Hauswedell <[email protected]>
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Maintainer: Hannes Hauswedell <[email protected]>
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License: AGPL v3
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Copyright: 2013-2020, Hannes Hauswedell; 2016-2020 Knut Reinert, FU-Berlin
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Copyright: 2013-2023, Hannes Hauswedell; 2016-2023 Knut Reinert, FU-Berlin
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Status: under development
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Description: Lambda is a biological sequence aligner optimized for many
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query sequences and searches in protein space. It is highly compatible
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to BLAST (bitscore and e-value statistics, tab separated and verbose
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output formats), much faster than BLAST and many other comparable tools
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and supports many other input and output formats, including standards-
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conformant .sam and .bam and many compression types
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Description: Lambda is a biological sequence aligner for searches
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in protein, nucleotide or bisulfite-treated databases. It is highly
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compatible to BLAST (bitscore and e-value statistics, tab separated and
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verbose output formats), much faster than BLAST and many other comparable
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tools and supports many other input and output formats, including
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standards-conforming .sam and .bam and many compression types.

‎LICENSE.rst

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================
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::
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Copyright (c) 2013-2020, Hannes Hauswedell
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Copyright (c) 2019-2020, Sara Hetzel
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Copyright (c) 2013-2023, Hannes Hauswedell
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Copyright (c) 2019-2023, Sara Hetzel
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All rights reserved.
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Lambda is *free software*: you can redistribute it and/or modify
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==========
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When Lambda is distributed in binary form or when Lambda is distributed
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in source form including its submodules the following additional
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license terms apply.
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Note that these submodules might themselves include further submodules, please see the respective license files.
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SeqAn copyright
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---------------
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::
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Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
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SeqAn is published under the terms of the three clause BSD license as can
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be found in the file `submodules/seqan/LICENSE <./submodules/seqan/LICENSE>`__
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or printed by the parameter ``--copyright``.
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SeqAn3 copyright
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---------------
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::
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Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
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Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
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SeqAn3 is published under the terms of the three clause BSD license as can
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be found in the file `submodules/seqan3/LICENSE.md <./submodules/seqan3/LICENSE.md>`__
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or printed by the parameter ``--copyright``.
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in source form including its submodules, additional license terms apply.
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See the respective files in the submodules folder:
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* submodules/biocpp-core/LICENSE.md
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* submodules/biocpp-io/LICENSE
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* submodules/cereal/LICENSE
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* submodules/fmindex-collection/TODO
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* submodules/seqan/LICENSE
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* submodules/sharg-parser/LICENSE.md

‎README.rst

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Lambda: the Local Aligner for Massive Biological DatA
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-----------------------------------------------------
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Lambda is a local aligner optimized for many query sequences and searches in protein space. It...
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Lambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...
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* is highly compatible to BLAST (bitscore and e-value statistics, tab separated and verbose output formats)
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* is highly compatible to BLAST (bit-score and e-value statistics, tab separated and verbose output formats)
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* is much faster than BLAST and many other comparable tools
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* supports many other input and output formats, including standards-conformant ``.sam`` and ``.bam`` and many compression types
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* supports many other input and output formats, including standards-conforming ``.sam`` and ``.bam`` and many compression types
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* has special features for species annotation and taxonomic analysis
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* is well-documented and easy to use (e.g. provides progress-bars and memory usage estimates)
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::
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% bin/lambda2 mkindexp -d db.fasta
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% bin/lambda3 mkindexp -d db.fasta
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*(in case you want to create a nucleotide index, instead use ``mkindexn``)*
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After that running Lambda is as simple as
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::
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% bin/lambda2 searchp -q query.fasta -i db.fasta.lambda
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% bin/lambda3 searchp -q query.fasta -i db.fasta.lambda
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*(in case you want to perform a nucleotide search, instead use ``searchn``)*
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For a list of options, see the help pages:
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::
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% bin/lambda2 --help
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% bin/lambda2 COMMAND --help
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% bin/lambda3 --help
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% bin/lambda3 COMMAND --help
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Advanced options are available via ``--full-help`` or the man pages, and more documentation is available
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in the `wiki <https://github.com/seqan/lambda/wiki>`__.
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authorship and copyright
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------------------------
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Lambda is being developed by `Hannes Hauswedell <mailto:[email protected]>`__, but it incorporates a lot of work from other members of the `SeqAn project <http://www.seqan.de>`__.
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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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| :width: 76px | |
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+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
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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 |
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| :alt: Newsletter | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is on average less than one e-mail |
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| :target: https://lists.fu-berlin.de/listinfo/lambda-users | per month. |
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| :alt: Newsletter | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is very low traffic! |
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| :target: https://lists.fu-berlin.de/listinfo/lambda-users | |
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| :width: 76px | |
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+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
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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. |

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