Building accurate SVDquartets-based species trees
To build SVDquest you can run
bazel build //src:SVDQuest -c opt
You can install the bazel build system here. Once the build is complete, your executable will be located at bazel-bin/src/SVDQuest.
Ideally, you will have wine installed, and the Windows version of PAUP*. The Windows version has better numerical routines and returns substantially more accurate trees than the Linux version.
To check if this is installed correctly, if you run wine paup4c from your command line, it should start PAUP*.
Alternatively, you can use the Linux version of PAUP*. In this case you should run SVDquest with the --nowine option.
If you are running on Windows or using the Linux version of PAUP* on Linux, you can specify a custom PAUP* executable using the --paup-exe option followed by the path to the executable.
You also need ASTRAL in the same folder as SVDquest. So if you are in the folder with the SVDquest executable, Astral/astral.4.7.8.jar (or any other version of ASTRAL) should exist.
To run SVDquest*, run
SVDquest -i <input gene trees> -a <input alignment> -o <output file>
SVDquest* 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:
SVDquest --score -a <input alignment> -o <output file>
If your analysis has a small number of taxa (perhaps less than 15), you can pass the --unconstrained option to SVDquest to do a global exact search. This will be (substantially) slower than the standard analysis, but it will likely provide a better result.