Canopy

Snippy — rapid haploid variant calling pipeline for bacterial genomics. Maps paired-end or single-end reads to a reference genome using BWA-MEM and Minimap2, calls SNPs, MNPs, and indels via Freebayes

3 shared topics • 2 shared operations

BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

2 shared topics • 3 shared operations

Dendroscope — interactive viewer for large phylogenetic trees and rooted networks. Handles hundreds of thousands of taxa with smooth navigation. Supports Newick, Nexus, and phyloXML input; exports PNG

2 shared topics • 3 shared operations

MetaPhlAn 4 + StrainPhlAn 4 — marker-gene-based metagenomic profiling and strain-level phylogenetics. MetaPhlAn profiles microbial communities at species level from shotgun metagenomes using ~5.1M uni

2 shared topics • 3 shared operations

Battenberg is an R package for allele-specific subclonal copy number analysis from whole-genome sequencing (WGS) tumor/normal paired BAM files. It segments the genome into clonal and subclonal copy nu

3 shared topics • 1 shared operation