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| executable | documentation | publication | |
| dotplot.pl blast2dotplot.pl exons2dotplot.pl | dependencies: linux OS, bl2seq | non | |
| proteinortho_v2.3.0.pl | documentation: computes genomwide orthologies by "reciprocal pairwise best blast", "fuzzy reciprocal blast" or a customized method. dependencies: linux OS, blastall, formatdb | non | |
| WagnerTest.pl WagnerTest_plot.pl | documentation | Guenter P. Wagner, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler. 2004. Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests. Mol.Biol.Evol. 21: 2116-2121 (2004) | |
| aln_order_v2.0.pl | documentation: computes minimum spanning tree and minimum hamiltonian path from a distance matrix. Alternatively, also computes the distance matrix from the alignment and a scoring matrix of your choice. dependencies: linux or Mac OS | non |