Pinned Repositories
hiv-founder-id
Estimate founders of HIV-1 infection using nucleotide sequences from very acute infection
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!
CQAPaper
Reproducible research directory for paper on the Quadratic Ascent algorithms CQA and UQA, which are implemented in the galosh/profillic github repo.
HIV-integration
PREAST
scripts for HIV-1 founder inference and time of infection estimation
siever
R code implementing sieve analysis methods
tsic2
Bayesian estimation of infection time from clinical diagnostic test assay results from early infection, an implementation of the Infection Dating Tool method due to Grebe et al, with modifications
profillic-hmmer
Modified versions of HMMER 3 programs to implement interoperability with galosh profiles (as generated by profillic).
profillic
A suite of programs for estimating parameters of Profile HMMs using Baum-Welch, Conditional Baum-Welch, and both Unconditional and Conditional Quadratic Ascent.
profuse
A suite of programs for working with Profile HMMs.
pedlefsen's Repositories
pedlefsen/tsic2
Bayesian estimation of infection time from clinical diagnostic test assay results from early infection, an implementation of the Infection Dating Tool method due to Grebe et al, with modifications
pedlefsen/hiv-founder-id
Estimate founders of HIV-1 infection using nucleotide sequences from very acute infection
pedlefsen/PREAST
scripts for HIV-1 founder inference and time of infection estimation
pedlefsen/CQAPaper
Reproducible research directory for paper on the Quadratic Ascent algorithms CQA and UQA, which are implemented in the galosh/profillic github repo.
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!
pedlefsen/siever
R code implementing sieve analysis methods
pedlefsen/HIV-integration