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
All mothur.shared files are a type of indexed data file. This is where the OTU clusters are defined – the cluster label, how many sequences, what that representative sequence is, and some statistics.
First, you’ll have an original shared file with everything, then you’ll filter it for significance to create the version used with the other downstream tools.
The example in this protocol is in the tutorial I linked. If you browser keyword search that page with “make.shared”, you’ll see where the original file was created, then all the other tools that use it.
Then for this part:
You can do two primary things to learn how a tool works.
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Review the original Mothur guides. Find these linked in the Help of the tool form or just browser search the suite name or tool name.
This works for most tools, and you’ll usually find lots of discussion since people use this tool everywhere and it works same. Definitely consider this when tuning parameters. The only difference in Galaxy is that you can access the tool through a web browser. Once you submit a job, it routes to a computer cluster that runs the same command as someone would use directly on the command line. You can even inspect this command on the Job Details page (pencil icon → tab into Details).
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Review any tutorials that include the tool. These might be from the original author or at other public scientific forums (same as above), or the tool might be included in a Galaxy tutorial (check the bottom of tool forms).
Tutorials can walk you through an example analysis with toy data. The tutorial files will have the same content and format as full sized files. Most have a workflow that you can use as a template, too. For complicated analysis, it is helpful to load up the tutorial data and run the workflow to create an answer key example history to compare too. This will allow you to examine all the intermediate files in detail.
I have an example here if you want to import to review the files. The last dataset is extra – I converted the mothur.shared file to a tabular format to make it easier to see the content.
Overall – what to do depends on what your data looks like now. There might be other tools and manipulations you can apply. Hope this helps and let us know how this goes!