Software & Tools

We maintain data and code for reproducibility in version-controlled in-house repositories for project-specific custom code, and in public repositories for software with broader applicability and to support transparent data science. We take pride in our software engineering and programming expertise. We develop tools that are useful to us and our collaborators. Our tools are research-grade and although we do not provide ongoing software support, we will work with you to help adapt our tools to specific use cases. This list represents a selection of our publicly hosted projects.


 Labuschagne PJL, Moshadi-Hossein A, Magaret CA, Holzman T, Edlefsen PT. siever: Software and algorithms for genomic analysis of breakthrough infections in HIV-1 vaccine trials. 2016.


Edlefsen PT. hiv-founder-id: Software for automated estimation of the founder sequence(s) of an HIV-1 infection, and the timing of that infection. 2015.


Edlefsen PT. profillic-hmmer: Modified versions of HMMER 3 programs to implement interoperability with galosh profiles (as generated by profillic). 2011.


Edlefsen PT. profillic: A suite of programs for estimating parameters of Profile HMMs using Baum-Welch, Conditional Baum-Welch, and both Unconditional and Conditional Quadratic Ascent. 2011.


Edlefsen PT. profuse: A suite of programs for working with Profile HMMs. 2011.


Edlefsen PT. prolific: A library of useful C++ classes for working with genomic sequence data and Profile HMMs. 2011.


Edlefsen PT, Holmes I, Rubin GM, Lunter G. HMMoC-BFloat-Algebra: A tiny C++ library for polymorphic representation of non-negative floating point values, including the Buoyant Float (BFloat) fixed-precision, arbitrary-range type. 2011.


Christmas R, Edlefsen PT. GINY Graph Interface Library: the low-level network API used by Cytoscape. 2004.


Major Contributors to BioPerl [Including Edlefsen PT]. BioPerl. 2003.


Generic Model Organism Database Project Development Team [Including Edlefsen PT]. GBrowse genome browser. 2003.


Edlefsen PT. Community Services for the Biologically Inclined: A platform for integrating data and software for molecular biology. 2003.


The MicroArray Gene Expression Database Group (MGED) [Including Edlefsen PT]. MAGEstk: The MAGE Software ToolKit, a suite of software for handling MicroArray Gene Expression (MAGE) data. 2002.