available at github.com/neherlab/treetime
TreeTime provides routines for ancestral sequence reconstruction and the inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the locations of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.
TreeTime aims at striking a compromise between sophisticated probabilistic models of evolution and fast heuristics. It implements GTR models of ancestral inference and branch length optimization, but takes the tree topology as given. To optimize the likelihood of time-scaled phylogenies, treetime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstrained nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool or as a library used in larger phylogenetic analysis workflows.
- ancestral sequence reconstruction (marginal and joint maximum likelihood)
- molecular clock tree inference (marginal and joint maximum likelihood)
- inference of GTR models
- rerooting to obtain best root-to-tip regression
- auto-correlated relaxed molecular clock (with normal prior)
PanX: pan-genome visulization and exploration
code on github.com/neherlab
PanX consists of a pipeline to identify bacterial pan-genomes and visualize them in a web browser. PanX can be used as a web application, or a stand-alone tool on a desktop. The visualization allows the user to explore relationships between phenotypic traits, the species phylogeny, and individual gene trees.
available at github.com/blab/nextflu
nextflu is designed to perform near real-time tracking of influenza virus evolution. It's divided into two components: augur, which takes a
.fasta file of flu sequences and builds an annotated phylogeny, and auspice, which displays this annotated phylogeny in an interactive web-based visualization.
The current version of nextflu is focused on tracking seasonal influenza H3N2 evolution in humans, looking at sequences from the hemagglutinin (HA) gene. Future versions may extend this analysis to other genes in H3N2 or other influenza subtypes. We would also like to implement formal predictive models to make nextflu a platform for forecasting evolution in addition to up-to-date tracking.
available at github.com/neherlab/ffpopsim
FFPopSim is a C++ and Python library to simulate large populations that are polymorphic at many loci. It allows for asexual and recombining populations and complex fitness functions, including pairwise and higher order epistasis. It is designed to study the effects of linked selection, the rare processes in large populations, and can be used to address a large variety of population genetics problems.
available at github.com/neherlab/PoissonNMF
PoissonNMF is an ImageJ plugin for blind spectral deconvolution of fluorescence microscopy images with multiple labels. It combines non-negative matrix factorization algorithms and a probabilistic treatment of photon shot noise.
Nicholas Noll, Marco Molari, Liam Shaw and Richard Neher
Microbial Genomics, in press., 2022.02.24.481757. 10.1101/2022.02.24.481757 bibtex
Pierre Barrat-Charlaix, Timothy G. Vaughan and Richard A. Neher
PLOS Computational Biology, 18 e1010394. 10.1371/journal.pcbi.1010394 bibtex
Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher
Journal of Open Source Software, 6 3773. 10.21105/joss.03773 bibtex
John Huddleston, James Hadfield, Thomas R. Sibley
Journal of Open Source Software, 6 2906. 10.21105/joss.02906 bibtex
Vadim Puller, Pavel Sagulenko and Richard A. Neher
Virus Evolution, 10.1093/ve/veaa066 pdf bibtex
Richard A. Neher and Trevor Bedford
Journal of Clinical Microbiology, 56 e00480--18. 10.1128/JCM.00480-18 pdf bibtex
James Hadfield, Colin Megill, Sidney M. Bell
Bioinformatics, 10.1093/bioinformatics/bty407 pdf bibtex
Pavel Sagulenko, Vadim Puller and Richard A. Neher
Virus Evolution, 4 vex042. 10.1093/ve/vex042 pdf bibtex
Wei Ding, Franz Baumdicker and Richard A. Neher
Nucleic Acids Research, 10.1093/nar/gkx977 pdf bibtex
Richard A. Neher and Trevor Bedford
Bioinformatics (Oxford, England), 31 3546--3548. 10.1093/bioinformatics/btv381 pdf bibtex
Fabio Zanini and Richard A. Neher
Bioinformatics (Oxford, England), 28 3332--3333. 10.1093/bioinformatics/bts633 pdf bibtex
Richard A. Neher, Miso Mitkovski, Frank Kirchhoff
Biophysical journal, 96 3791--3800. 10.1016/j.bpj.2008.10.068 bibtex