I have a large dataset (>10,000) of 16S rRNA sequences. Rather than build a phylogenetic tree, I'd rather visualize the analysis on a 2D PCoA-like plot.
I plan to use a maximum likelihood method for the analysis and ultimately want to portray the data in a PCoA-like plot. Tree topology is not important for this. Is it possible to run an ML-based analysis and obtain just the resulting distance matrix? I'd like to use the matrix to create the PCoA plot. Also, is the dataset too large? Any suggestions of softwares?
The goal of this analysis is to evaluate the relatedness of select strains (~300) against a larger global population.
Really appreciate the help!