This program takes a NEXUS file containing aligned DNA sequences and recodes the gaps using the simple indel coding algorithm. It was developed for the study published in:
Ogden, T.H., and M.S. Rosenberg (2007) How should gaps be treated in parsimony? A comparison of approaches using simulation. Molecular Phylogenetics and Evolution 42(3):817–826.
The program is written in pascal and compiled with with free pascal compiler. Executables for linux and windows are both included in the repository. If you are interested in just running the program, download the IndelCoder.zip (Windows) or IndelCoder.tar.gz (Linux) files from the distribution directory.