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[doc] prep for release
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h-2 committed Jun 22, 2023
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18 changes: 9 additions & 9 deletions INFO
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Name: lambda
Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
Maintainer: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
Author: Hannes Hauswedell <h2@fsfe.org>
Maintainer: Hannes Hauswedell <h2@fsfe.org>
License: AGPL v3
Copyright: 2013-2020, Hannes Hauswedell; 2016-2020 Knut Reinert, FU-Berlin
Copyright: 2013-2023, Hannes Hauswedell; 2016-2023 Knut Reinert, FU-Berlin
Status: under development
Description: Lambda is a biological sequence 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), much faster than BLAST and many other comparable tools
and supports many other input and output formats, including standards-
conformant .sam and .bam and many compression types
Description: Lambda is a biological sequence aligner for searches
in protein, nucleotide or bisulfite-treated databases. It is highly
compatible to BLAST (bitscore and e-value statistics, tab separated and
verbose output formats), much faster than BLAST and many other comparable
tools and supports many other input and output formats, including
standards-conforming .sam and .bam and many compression types.
37 changes: 11 additions & 26 deletions LICENSE.rst
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================
::

Copyright (c) 2013-2020, Hannes Hauswedell
Copyright (c) 2019-2020, Sara Hetzel
Copyright (c) 2013-2023, Hannes Hauswedell
Copyright (c) 2019-2023, Sara Hetzel
All rights reserved.

Lambda is *free software*: you can redistribute it and/or modify
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==========

When Lambda is distributed in binary form or when Lambda is distributed
in source form including its submodules the following additional
license terms apply.
Note that these submodules might themselves include further submodules, please see the respective license files.

SeqAn copyright
---------------
::

Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin

SeqAn is published under the terms of the three clause BSD license as can
be found in the file `submodules/seqan/LICENSE <./submodules/seqan/LICENSE>`__
or printed by the parameter ``--copyright``.

SeqAn3 copyright
---------------
::

Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik

SeqAn3 is published under the terms of the three clause BSD license as can
be found in the file `submodules/seqan3/LICENSE.md <./submodules/seqan3/LICENSE.md>`__
or printed by the parameter ``--copyright``.
in source form including its submodules, additional license terms apply.
See the respective files in the submodules folder:

* submodules/biocpp-core/LICENSE.md
* submodules/biocpp-io/LICENSE
* submodules/cereal/LICENSE
* submodules/fmindex-collection/TODO
* submodules/seqan/LICENSE
* submodules/sharg-parser/LICENSE.md
20 changes: 10 additions & 10 deletions README.rst
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Lambda: the Local Aligner for Massive Biological DatA
-----------------------------------------------------

Lambda is a local aligner optimized for many query sequences and searches in protein space. It...
Lambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...

* is highly compatible to BLAST (bitscore and e-value statistics, tab separated and verbose output formats)
* 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-conformant ``.sam`` and ``.bam`` and many compression types
* 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)

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::

% bin/lambda2 mkindexp -d db.fasta
% 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/lambda2 searchp -q query.fasta -i db.fasta.lambda
% bin/lambda3 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
% 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 being developed by `Hannes Hauswedell <mailto:hannes.hauswedell@fu-berlin.de>`__, but it incorporates a lot of work from other members of the `SeqAn project <http://www.seqan.de>`__.
Lambda is developed by `Hannes Hauswedell <mailto:h2 (æð) fsfe.org>`__ and `Sara Hetzel <mailto:hetzel (æð) molgen.mpg.de>`__ .

+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| **Please always cite the publication, also if using Lambda in comparisons and pipelines** |
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| :width: 76px | |
+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. 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. |
| :alt: Newsletter | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is very low traffic! |
| :target: https://lists.fu-berlin.de/listinfo/lambda-users | |
| :width: 76px | |
+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. 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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