From OpenWetWareJump to navigationJump to search
Amphora-2 (Guillaume Jospin, Aaron Darling, Morgan Langille, Dongying Wu, Thomas Sharpton, Katie Pollard, Jonathan Eisen)
- AMPHORA-2 is a reworked version of AMPHORA to include newer tools and newer markers.
- 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.
- See/ask DY on how to put together sequences for 1 marker
- Pick Representatives. Test the different methods, need to agree on 1.
- Use the MCL approach
- Use the PD approach
- Use (a) consensus sequence(s) from HMMemit