Enhancing searches for optimal trees with SIESTA
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README.md

FastRFS

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

Running FastRFS

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:

  1. The path to the file must not have spaces
  2. The newick trees must not have branch lengths
  3. 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.

Building FastRFS

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.

Dependencies

You need to have the following installed on your computer (Ubuntu package names or URLs are listed):

Building

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