Download The Executable jar is available here

WARNING: the program is memory intensive! I won't recommend running it in on your desktop if you are running other applications.

The default edit distance threshold is 20, default rf threshold is 3

Usage

Currently the program only accepts FASTA input files.

Note that their is no GUI as of now, the only way to run it is using the command line, as follows:

"java -Xmx6g -cp stability.jar Main input.tre input.fa results-prefix [full] [edit-threshold rf-threshold]"

Please make sure you specify enough memory by using "-Xmx10g" or something similar depending upon your dataset.

Use "full" to force analysis of internal nodes, note that this may be time consuming.

You can specify an edit distance threshold, any nodes that require more editing than that will be considered stable

The software will generate a number of files with the prefix given as the 3rd parameter to the program:

Output files

worstmovables.txt : these are the nodes that were able to make the largest jumps, ranked

zscore_ranking.txt: this is the ranking of internal nodes using z-scores as described in the paper

innode-dictionary.txt: this define the clade of each of the internal nodes, useful for looking up movable clades etc.

zscore.csv: lists z-scores for all internal nodes

editToRF.csv: complete matrix of RF values for each edit distance threshold for each node

rfToEdit.csv: complete matrix of Edit Distance required to move values for each node

worst_case.txt: worst move possible for every node


If you have any problems please contact [lastname @ cise dot ufl dot edu]. Replace lastname with the last name below

Saad Sheikh