The following are software projects that have been produced in my lab:
Genome Sequence Software
MySSP
- 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. PDF
IndelCoder
- 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. Molecular Phylogenetics and Evolution 42(3):817–826. PubMed PDF (Erratum: 2008, 46(2):807–808 PDF)
Spatial Analysis Software
Meta-Analysis Software
Fail-Safe Number Calculator
- 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. Evolution 59(2):464–468. PubMed PDF