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.
Please see the cookbook. Warning: this documentation may not apply to older versions of LAST! You can see your version with:
lastal --version
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.
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: