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This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.
LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
IndelExtractor is a GUI and command-line application written in Perl that generates various molecular sequence alignment masks, including one to make identification and removal of Indels and their surrounding ambiguous alignment quick and simple.