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LAST: find & align related regions of sequences
===============================================
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LAST is designed for moderately large data (e.g. genomes, DNA reads,
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proteomes).  It's especially good at:

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* Finding rearrangements and recombinations: we believe last-split_
  does that more rigorously than anything else.
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* Finding DNA-versus-protein related regions, especially protein
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  fossils (but introns are not considered).

* Unusual data, e.g. AT-rich DNA, because we can fit_ parameters to
  the data and calculate significance_.

* Sensitive DNA-DNA search, due to fitting_, sensitive seeding_, and
  calculating significance_.

It can also: indicate the confidence/uncertainty of each column in an
alignment, and use sequence quality data in a rigorous fashion.
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Usage
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-----

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Please see the cookbook_.  **Warning:** this documentation may not
apply to older versions of LAST!  You can see your version with
``lastal --version``.
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Install
-------
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Please download the highest version number from
https://gitlab.com/mcfrith/last/-/tags.  Using the command line, go
into the downloaded directory and type::
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  make
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This assumes you have a C++ compiler.  On Linux, you might need to
install a package called "g++".  On Mac, you might need to install
command-line developer tools.  On Windows, you might need to install
Cygwin.  (It's possible to specify a compiler like this:
``make CXX=MyOtherCompiler``.)
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The programs are in the ``bin`` directory.  For convenient usage, set
up your computer to find them automatically.  Some possible ways:
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* Copy the programs to a standard directory: ``sudo make install``
  (using "sudo" to request administrator permissions).
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* Copy the programs to your personal bin directory: ``make install prefix=~``
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* Adjust your `PATH variable`_.
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You might have to log out and back in before your computer recognizes
the new programs.

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**Alternative:** Install LAST from bioconda_.  But it might not be the
latest version: usually that doesn't matter, but it might work
inferiorly or differently from this documentation.
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Further info
------------
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Details & citation: `LAST papers`_
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LAST is distributed under the GNU General Public License, either
version 3 of the License, or (at your option) any later version.
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LAST is brought to you by:
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* `Computational Omics Research Team`_, AIRC_
* GSFS_, `University of Tokyo`_
* `AIST-Waseda University CBBD-OIL`_
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.. _fit:
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.. _fitting: doc/last-train.rst
.. _last-split: doc/last-split.rst
.. _seeding: doc/last-seeds.rst
.. _significance: doc/last-evalues.rst
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.. _cookbook: doc/last-cookbook.rst
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.. _LAST papers: doc/last-papers.rst
.. _bioconda: https://bioconda.github.io/
.. _PATH variable: https://en.wikipedia.org/wiki/PATH_(variable)
.. _Computational Omics Research Team: https://www.airc.aist.go.jp/en/cort/
.. _AIRC: https://www.airc.aist.go.jp/en/
.. _GSFS: https://www.k.u-tokyo.ac.jp/index.html.en
.. _University of Tokyo: https://www.u-tokyo.ac.jp/en/
.. _AIST-Waseda University CBBD-OIL: https://unit.aist.go.jp/cbbd-oil/en/