Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

⚡ TabPFN: Foundation Model for Tabular Data ⚡

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Rust package for constructing and analyzing phylogenies.

Rust for data analysis encyclopedia (WIP).

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide a small …

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Assembly based core SNP alignments

✂️ ⚡ Rapid haploid variant calling and core genome alignment

A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

🧬 An R package for visualizing molecular data in 3D

Visualize and interact with Protein Data Bank (pdb) and structural files in R and Shiny