FairShapley.pl 30/07/2015 Kristina Wicke and Mareike Fischer DESCRIPTION ------------------- This tool computes the Fair Proportion Index and/or different versions of the Shapley Value for phylogenetic trees in the Newick format (for information on the Newick tree format, please see http://evolution.genetics.washington.edu/phylip/newicktree.html ). For rooted trees you can choose between the Fair Proportion Index, the original Shapley Value, the modified Shapley Value and the unrooted Shapley Value on rooted trees. For unrooted trees only the original Shapley Value can be calculated (since the Fair Proportion Index is only defined for rooted trees and the modified Shapley Value coincides with the original Shapley Value in this case). ----------------------------------------------------------------------------------------------------------------------------------------------------- REQUIREMENTS ------------------- FairShapley.pl is written in the programming language Perl, including modules from BioPerl. Modules needed to run the script are: strict (a perl pragma to restrict unsafe constructs) warnings (a perl pragma to control optional warnings) Getopt::Long (command line arguments) Try::Tiny (error handling) Bio::TreeIO Bio::Tree::Tree Bio::Tree::Node Please make sure, that Perl, BioPerl and the modules mentioned above, are installed on your machine. For further information on installation see http://www.cpan.org/modules/ . ----------------------------------------------------------------------------------------------------------------------------------------------------- RUNNING THE SCRIPT ------------------- To execute FairShapley.pl, please call ~$./FairShapley.pl --in=filename (--out=filename) (--values=value) (--help) where ~$ denotes the directory, where the file FairShapley.pl is stored. An input file, containing one or several phylogenetic trees, in the Newick tree format, must be given in any case, while the following arguments are optional: --out=filename Generates an output file containing the computed values (otherwise the results are printed to the shell). --values=value Choose the diversity index to calculate. Options for value: 0 Calculation of FP 1 Calculation of SV (modified SV if the tree is rooted, original SV if the tree is unrooted) 2 Calculation of FP and SV unrooted on rooted trees 3 Calculation of FP and (modified) SV Per default the FP and the (modified) SV are calculated (option 3). --help Example: ~$./FairShapley.pl --in=myTree --out=myResults --values=0 ----------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------- FairShapley.pl can be reached at: web site: www.mareikefischer.de/Software/FairShapley.pl E-Mail: kristina.wicke@stud.uni-greifswald.de, email@mareikefischer.de