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
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:
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