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.
Links
- AMPHORA – OpenWetWare
- Paper: Genome Biology | Full text | A simple, fast, and accurate method of phylogenomic analysis
- Software available at Figshare here.
Examples of using AMPHORA
Jonathan Eisen's Lab 
Thanks for releasing AMPHORA. I was excited to give it a shot, making it as far as the dependency on WU-BLAST when I hit a wall. Apparently, WU-BLAST is now a commercial product, and one that I frankly can’t support in light of its fork from the public project upon which it was based. (I know Gish did a lot of that initial work, but he did it with public money!) Ranting aside, is there any way to sidestep the WU-BLAST requirement (e.g. with standalone NCBI BLAST)?
LikeLike
My lab has not been working on AMPHORA anymore as Martin Wu kind of took that with him to a faculty job at UVA. We have been contributing to Phylosift http://phylosift.wordpress.com
LikeLike
Thanks for the quick reply. We’re looking to build robust trees for finished genomes, so it looks like AMPHORA 2 may be our best bet. I really like what I see of the Phylosift project, and if we have a need to characterize environmental samples in the future, we’ll definitely give it a try.
Thanks,
Dave
LikeLike