Survival analysis in Python
Image-processing software for cryo-electron microscopy
RAxML Next Generation: faster, easier-to-use and more flexible
Efficient phylogenomic software by maximum likelihood
CmdStanR: the R interface to CmdStan
Comparative Genomics Toolkit 3
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Maximum likelihood demultiplexing
Maximum Likelihood estimation and Simulation for Stochastic Differential Equations (Diffusions)
Gauss Naive Bayes in Python From Scratch.
Matlab package for learning to specify, compute, and estimate dynamic discrete choice models
spatialreg: spatial models estimation and testing
Python Rust implementation of the Probabilistic Principal Component Analysis model
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
Channel estimations based on RLS, LMS and ML methods.
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Python notebooks for my graduate class on Detection, Estimation, and Learning. Intended for in-class demonstration. Notebooks illustrate a variety of concepts, from hypothesis testing to estimation to image denoising to Kalman filtering. Feel free to use or modify for your instruction or self-study.
TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
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