Alignment
To understand the evolutionary relationships between the sequences in the sample and to perform a diversity analysis, it is necessary to generate a phylogenetic tree of the OTUs. The first step in generating the tree is to generate a multiple alignment of the representative OTU sequences. PyNAST aligns the sequences to a template alignment of reference 16S sequences. INFERNAL makes use of a Hidden Markov Model that also incorporates secondary structure information.
Software: PyNAST, INFERNAL
Bibliography
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.