pedlefsen/CQAPaper
Reproducible research directory for paper on the Quadratic Ascent algorithms CQA and UQA, which are implemented in the galosh/profillic github repo.
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Discovered Oct 21, 2026
pedlefsen / hiv-founder-id
Estimate founders of HIV-1 infection using nucleotide sequences from very acute infection
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pedlefsen/HMMoC-BFloat-Algebra
A tiny C++ library supplying the Algebra<> template, for polymorphic representation of non-negative floating-point values in either native (eg double), log-transformed, or BFloat representations. BFloat is the Buoyant Float type, allowing fixed-precision representation at an arbitrary precision range. The library is based on code from: Lunter G. HMMoC—a compiler for hidden Markov models. Bioinformatics (2007) 23(18): 2485-2487. The code was derived by Ian Holmes and Gerton Lunter from Holmes I, Rubin GM. An expectation maximization algorithm for training hidden substitution models. J Mol Biol. 2002 Apr 12;317(5):753-64. You may use at will, subject to the license, but *please cite those two papers* in your academic publications associated with uses of this library. Thank you!