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Updated Home (markdown)
remove disclaimer
add warning about removed sequences
Fix link name to expandflag
add link to expandflag task page
add link to micplot
replace antibiotic -> antimicrobial
Add pubmlstget to task list
Add pubmlstpsecies to task list
Add link to MLST calling page
Remove link to reportfilter page because the task no longer exists
Fix brackets typo
link to getref instead of listing all the dbs
add plasmidfinder link
typo in phandango filename
add link to refquery page
fix synopsis for release 2.0.0
Reword: ref seqs are not necessarily genes
name other supported references
add disclaimer
Link to aln2meta page
Add Phndango to synopsis
Link to CARD
Write synopsis and list links to tasks
Move description of run task to a separate file
Move summary info to separate file
Move flag info into separate file
tweak summary number 2 description
Update flag and summary numbers
Update flag example