| Name (home page) | Description | Source Code (repository) | Author(s) | Institution(s) |
|---|---|---|---|---|
| Paloverde | 3D Tree visualization for large trees | C, OpenGL | Sanderson | U of Arizona |
| gtp | Calculation of gene duplication scores for a set of gene trees reconciled against a given species tree (see Sanderson and McMahon 2007) | C | Sanderson | U of Arizona |
| blink | Constructs single linkage clusters from a 'hit list' of pairwise hits | C | Sanderson | U of Arizona |
| blast2blink | Generate a 'hit list' of pairwise hits by processing BLAST output (see McMahon and Sanderson 2006) | Perl | McMahon | U of Arizona |
| grovify | Constructs groves of phylogenetic trees based on taxon overlap graph (see Sanderson et al. 2007; Ane et al. 2008) | Perl | McMahon | U of Arizona |
| orthologizer | Phylogenetic test of orthology (see Sanderson et al. 2003) | Perl | McMahon, Cranston | U of Arizona |
| Biclique finder | Exact enumaration of all bicliques in a graph (e.g., taxon by cluster graph) (implementation of Alexe et al. algorithm; see Sanderson et al. 2003) | C++ | Chang | Iowa State |
| Phylota Browser Database | Scripts to set up database and user interface (see Sanderson et al. 2008) | Perl | Sanderson | U of Arizona |
| Phylota Browser Database | Reverse indexed search of trees in the database (see Chen et al. 2008) | C++, Perl | Chen | Iowa State |
| Phylota Browser Database | LCA query algorithm (see Sanderson et al. in review) | C++, Perl | Wehe | Iowa State |
| fastgenedup | Build species trees using gene duplication scores and a collection of gene trees(see XXXX) | C++ | Wehe, Bansal | Iowa State |