phylogenetics tools for linux (and other mostly posix compliant) computers
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Updated
Jun 20, 2024 - C++
phylogenetics tools for linux (and other mostly posix compliant) computers
Comparative Genomics Toolkit 3
A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).
phylogenetic analyses informed by deep mutational scanning data
Molecular Evolution Library for Python
Phylotranscriptomic analysis pipeline
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
*Monteagudo-Cascales E., *Gumerov V.M., Fernández M., Matilla M.A., Gavira J.A., Zhulin I.B., Krell T. (2024) Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria.
A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.
An R package to identify and classify duplicated genes from whole-genome protein sequence data
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
Janani Ravi's Research Group
A tool for plotting CAFE5 gene family expansion/contraction result
Homepage of Dr Stephen P. Moss, Computational Scientist
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
V. M. Gumerov, E. P. Andrianova, M. A. Matilla, Karen M. Page, Elizabet Monteagudo-Cascales, A. C. Dolphin, T. Krell, I. B. Zhulin (2022). Amino acid sensor conserved from bacteria to humans.
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