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A small program that glues together other programs allowing a user to input a codon alignment in FASTA format and produce an annotated phylogenetic tree showing which substitutions occurred on a gi…
Java Image Processing Pipeline (JIPipe) is a graphical batch processing language for the ImageJ ecosystem
Open copy of the CBS Tools software repository
For all your cluster needs
Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3
Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.
A feature rich and easy to use phylogenetic tree editor
BEAST2 implementation of the Masco approximation of the structured coalescent with forwards/backwards algorithm for node state calculation
An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.
Source code for TreeBASE web application and database
Multi-type birth-death-sampling modelling for BEAST 2.
This BEAST2 package provides MCMC proposals and post-processing tools for sampling trees containing sampled ancestors
Beast2 implementation of the coalescent with reassortment
Implementation of the site-wise mutation-selection model (swMutSel) described in Tamuri et al. (2012, 2014) , and Tamuri and dos Reis (2022)
A package for BEAST 2 implementing generally useful stuff
repository for code and releases of PIQMEE add-on for BEAST2
Software and data used in Tamuri AU, dos Reis M, Hay AJ, Goldstein RA (2009) Identifying Changes in Selective Constraints: Host Shifts in Influenza. PLoS Comput Biol 5(11): e1000564 doi:10.1371/jou…
Phylodynamic simulations of influenza virus evolution with antigenic and deleterious mutations, implented in Java. This is a modified version of Trevor Bedford's program Antigen (http://bedford.io/…