Getting help with FastRFS
If you're having problems with FastRFS, you can:
Join the user group at https://groups.google.com/forum/#!forum/fastrfs-users/
File an issue on GitHub
Email me: vachasp2 at illinois dot edu
Download the FastRFS executable from the Releases page (https://github.com/pranjalv123/FastRFS/releases).
The simplest way to run FastRFS is like
FastRFS -i sourcetrees.newick
where sourcetrees.newick is the path to a file containing your source trees in newick format.
Currently, this file must have the following properties:
- The path to the file must not have spaces
- The newick trees must not have branch lengths
- The newick trees must be compatible with ASTRAL-II
FastRFS will output the score (total RF distance to the input trees) and the output tree to the command line.
To save this tree to a file, run
FastRFS -i sourcetrees.newick -o outputfile
To add extra trees to expand the search space (the set X) of your analysis, run
FastRFS -i sourcetrees.newick -e extratrees.newick
The extratrees file should be in the same format as sourcetrees.newick, except that it is OK if it has branch lengths.
You only need to do this if the FastRFS executable doesn't run on your system or you're making changes to the source code.
You need to have the following installed on your computer (Ubuntu package names or URLs are listed):
- Boost (libboost-all-dev)
- ASTRAL (https://github.com/smirarab/ASTRAL/)
Clone and cd into the repository, then do:
mkdir build/ cd build/ cmake ../src make
Then copy the ASTRAL installation into the directory with FastRFS