How can I make a phylip-formatted distance matrix? I need it for beta diversity analysis
For the Mothur tool Pcoa Principal Coordinate Analysis for a distance matrix (link at EU), you can create the file with the Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups tool (link at EU).
How to learn the expected into formats for tools is under accepted formats toggle near the the input area to the tool. The Mothur tools “usually” have an output format that is based on the upstream tool that generates it, so reviewing that common naming between tools is one place to start.
All the upstream tools and steps are in our tutorial here. → Hands-on: 16S Microbial Analysis with mothur (extended) / 16S Microbial Analysis with mothur (extended) / Microbiome (see #beta-diversity).
Hope this helps! 
Dear,
Thanks. But for using the Dist. shared, the file should be in the format mothur.shared. How can I change the format of my file to this format, and how can I understand the requirements and structure of each format?
Thanks