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Partially update doc version 2
Update Crotty GHOST ref
update citations
change dx.doi.org to doi.org
update command reference and likelihood mapping plots
update reference to Hoang et al in the documentation
update Home
change citation for UFBoot
Home update
Update ModelFinder citation
minor update
reformat
fix links
Update Home.md and tables
update headings
Added link to web server tutorial in the list
update
update command reference
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merge