TreeTime

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.

Features

• 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.

nextstrain

available at github.com/nextstrain

The Nextstrain project has the aim to facilitate real-time analysis of pathogen genomes. It encompasses a large number of tools that are mostly developed and maintained by the lab of Trevor Bedford in Seattle and our lab in Basel. Nextstrain is extensively documented at docs.nextstrain.org. It's major components are

• augur: a bioinformatics toolkit for phylogenetic analysis
• auspice: Interactive Tool for Visualising Phylogenomic Data
• Nextclade: a browser and CLI based tool for clade assignment, QC, and mutation calling
• nextstrain.org: the server that hosts the main Nextstrain site.

FFPopSim

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.

PoissonNMF

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.