protein-evolution

A Julia package to analyze protein sequences, structures, and evolutionary information

Analyzing combinations of codon substitution histories

phylogenetic analyses informed by deep mutational scanning data

Use Thor's Axe to cut exons into their evolutionary building blocks ⚡

A tool to model the evolution and structural impact of alternative splicing

Learning the language of phylogeny with MSA Transformer

Comparative evolutionary analysis of recurrent human TP53 cancer mutation hotspots across 56 mammalian species, integrating residue-level conservation, statistical testing, phylogenetic analysis, and cancer-associated mutation data to investigate evolutionary constraints on clinically relevant TP53 residues.

Automated pipeline for downloading, cleaning, and analyzing mainly alpha-helix protein structures from the CATH database.

Exploring evolutionary protein fitness landscapes

Artificial intelligence-driven framework for discovering synthetic binding protein-like scaffolds from the entire protein universe

Evolutionary and comparative analysis of vertebrate TP53 proteins using multiple sequence alignment, conservation analysis, and phylogenetic reconstruction.

Code-base for my ABC-selectivity paper in Current Biology

Phylogeny and classification of Azolla filiculoides MYB genes

Phylogenetic tree of LAR and other PIP family enzymes as shown in Güngör et al. 2020. This repository details all code and intermediate files used.

Code and Data for Research Article

Phylogenetic analysis of SMC proteins (cohesin, condensin, SMC5/6) across 14 eukaryotes from all major supergroups