ancient pathogen screening workflow

Code to reproduce analyses in Kim et al. 2024

Infering ancestral synteny with hierarchical orthologous groups

Discovery of conserved gene clusters in multiple genomes

Scripts to make using MIA (mapping-iterative-assembler) easier

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Logan Unitigs and Contigs

A web interface for querying biological sequence indexes

Massively parallel phylogenetic placement of genetic sequences

Bayesian reconstruction of ancient DNA fragments

Precise host read removal

Create fancy (bokeh) gene locus plots from GenBank files!

Panaln: Indexing pangenome for read alignment

MEM Pangenome Injection Genotyping

COsine-based SImilarity Genotyper using pangenomes

Per-position conservation index of multiple sequence alignment

Print or check MD5 checksums.

A very fast interval tree data structure

An aDNA aware short-read mapper

Evolutionary Transcriptomics with R

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning