ASTRAL-SIESTA
A version of the ASTRAL algorithm that returns multiple optimal trees using the SIESTA technique
To build ASTRAL-SIESTA you will first need phylokit and phylonaut,
mkdir build
cd build
cmake ../src
make
You also need ASTRAL in the same folder as ASTRAL-SIESTA. So if you are in the folder with the SVDquest executable, there should be a file at the path Astral/astral.*.jar, with the exact name depending on the ASTRAL version
To run ASTRAL-SIESTA, run
ASTRAL-SIESTA -i <input gene trees> -a <input alignment> -o <output file>
ASTRAL-SIESTA* uses SIESTA to generate strict, greedy, and majority consensus trees of all optimal trees, as well as a single arbitrarily chosen optimal tree. If for some reason this is a problem, you can disable these with --nogreedy, --nostrict, and --nomajority options.
You can also use the --score option to score a tree like this:
ASTRAL-SIESTA --score -a <input alignment> -o <output file>