AMPHORA is an Automated Phylogenomic Inference Pipeline for bacterial sequences. From a given a set of protein sequences, it automatically identifies 31 phylogenetic marker genes. It then generates high-quality multiple sequence alignments for these genes and make tree-based phylotype assignments.
- AMPHORA – OpenWetWare
- Paper: Genome Biology | Full text | A simple, fast, and accurate method of phylogenomic analysis
- Software available at Figshare here.