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Add Newick tree output options
Extend tree output option information
Minor refinement in filefix option description
Refine output options and add merge command
Refine all option tables, and add filter
Add output prefix/suffix and compression
Add citation and gz doc
Update doc for new version
Update wiki to new global command structure.
Update CLI Formatter.
Add KR distance command
Add Edge PCA doc.
Add squash clustering.