A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
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Updated
May 14, 2024 - Python
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Comparative Genomics Toolkit 3
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
Microbial Genome Circular plotting tool for comparative genomics using Circos
DFOIL: Introgression Testing for Five Taxa
A tool for plotting CAFE5 gene family expansion/contraction result
Workflow for identifying and classifying homologous gene/protein sequences
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
project that enables molecular design and computational screening of small molecules
Molecular Evolution Library for Python
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.
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.
Calculate conditional probability distributions of extant sequences given a phylogenetic tree, sequence alignment, and evolutionary model.
A new model-selection criteria for phylogenetics to calculate the predictive log-likelihood score.
*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.
Phylotranscriptomic analysis pipeline
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