The following are software projects that have been produced in my lab:
- This program simulates DNA sequence evolution under a variety of conditions. It is described in:
- Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence
simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83.
- This program takes a NEXUS file containing aligned DNA sequences and recodes the gaps using
the simple indel coding algorithm. The program was developed for use in:
- Ogden, T.H., and M.S. Rosenberg (2007) How should gaps be treated in parsimony? A comparison
of approaches using simulation.
Phylogenetics and Evolution 42(3):817–826.
PDF (Erratum: 2008, 46(2):807–808 PDF)
- This program calculates fail-safe numbers for meta-analysis based on the methods described in:
- Rosenberg, M. S. (2005) The file-drawer problem revisited: A general weighted method for
calculating fail-safe numbers in meta-analysis.