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https://gitlab.com/mcfrith/last


https://gitlab.com/mcfrith/last

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LAST: find & align related regions of sequences

===============================================



LAST is designed for moderately large data (e.g. genomes, DNA reads,

proteomes).  It's especially good at:



* Finding rearrangements and recombinations: we believe last-split_

  does that more rigorously than anything else.



* Finding DNA-versus-protein related regions, especially protein_

  fossils_.



* 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.



Usage

-----



Please see the cookbook_.  **Warning:** this documentation may not

apply to older versions of LAST!  You can see your version with::



  lastal --version



Install

-------



You can install it from bioconda_ or `Debian Med`_, or like this...



Download the highest version number from

https://gitlab.com/mcfrith/last/-/tags.  Using the command line, go

into the downloaded directory and type::



  make



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.  You might also need to install something like "zlib-devel".



For ARM CPUs, the default "make" seems to work in some cases but not

others (sigh).  This seems to be good for ARM::



  make CXXFLAGS="-mcpu=native -O3 -pthread"



It's possible to specify a compiler like this: ``make CXX=MyOtherCompiler``.

If you re-run ``make`` in different ways, it may be good to do ``make clean``

first, to remove any previously-made files.



The programs are in the ``bin`` directory.  For convenient usage, set

up your computer to find them automatically.  Some possible ways:



* Copy the programs to a standard directory: ``sudo make install``

  (using "sudo" to request administrator permissions).



* Copy the programs to your personal bin directory: ``make install prefix=~``



* Adjust your `PATH variable`_.



You might have to log out and back in before your computer recognizes

the new programs.



Further info

------------



Details & citation: `LAST papers`_



LAST is distributed under the GNU General Public License, either

version 3 of the License, or (at your option) any later version.



LAST is brought to you by:



* `Computational Omics Research Team`_, AIRC_

* GSFS_, `University of Tokyo`_

* `AIST-Waseda University CBBD-OIL`_



.. _fit:

.. _fitting: doc/last-train.rst

.. _last-split: doc/last-split.rst

.. _seeding: doc/last-seeds.rst

.. _significance: doc/last-evalues.rst

.. _cookbook: doc/last-cookbook.rst

.. _LAST papers: doc/last-papers.rst

.. _protein: https://doi.org/10.1109/TCBB.2022.3177855

.. _fossils: https://doi.org/10.1093/molbev/msac068

.. _bioconda: https://bioconda.github.io/

.. _Debian Med: https://www.debian.org/devel/debian-med/

.. _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/