Software

alignfigR – R package to visualize large multiple sequence alignments
Written by Stephanie J. Spielman
Source  

codon_tools – Toolkit to manipulate synonymous codon usage in various ways
Written by Claus O. Wilke
Source   PyPI  

cowplot – Streamlined plot theme and plot annotations for ggplot2
Written by Claus O. Wilke
Source   CRAN  

parsemsf – Parse ThermoFisher MSF files and estimate protein abundances
Written by Benjamin R. Jack
Source   CRAN  

PeptideBuilder – Simple Python library to generate model peptides
Written by Matthew Z. Tien and Dariya K. Sydykova
Source   PyPI   Paper  

Pyvolve – Flexible Python module for simulating sequences along phylogenies
Written by Stephanie J. Spielman
Source   PyPI   Paper