Explore projects

searching and extracting universal single-copy genes from PhyloM:bacteria

building forests of near-ML trees

Estimating standard descriptive statistics from FASTQ files

Fast greedy clustering of genomes based on minhash similarity

majority-rule consensus of ML phylogenetic trees

Computing the probability that a phylogenetic tree is the result of a Yule process

Finding Repeats Using BLAST

Region segmentation

delineation cutoff estimates

Code and data for the article "Integrating information from historical data into mechanistic models for influenza forecasting" by Alessio Andronico, Juliette Paireau and Simon Cauchemez

Some helpers for my HTS snakemake workflows.

Smith-Waterman-based Average Nucleotide Identity