Comparative Genomics Toolkit 3
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Updated
Aug 5, 2024 - Python
Comparative Genomics Toolkit 3
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
DFOIL: Introgression Testing for Five Taxa
Microbial Genome Circular plotting tool for comparative genomics using Circos
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
Molecular Evolution Library for Python
project that enables molecular design and computational screening of small molecules
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.
Workflow for identifying and classifying homologous gene/protein sequences
A tool for plotting CAFE5 gene family expansion/contraction result
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Phylotranscriptomic analysis pipeline
A new model-selection criteria for phylogenetics to calculate the predictive log-likelihood score.
Simulate predictive datasets from MrBayes' output
A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.
*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.
Calculate conditional probability distributions of extant sequences given a phylogenetic tree, sequence alignment, and evolutionary model.
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