ViralMSA v1.1.14

• Added GUI
• Added log file to output directory

ViralMSA v1.1.13

• Added Unimap support
  • Unimap seems to be ~40x slower than Minimap2 (at least on the toy HIV dataset I tried), so the default choice in ViralMSA will remain Minimap2 (at least for now)

ViralMSA v1.1.12

• Fixed bug where long stretches of N cause a consensus sequence to get split and not show up entirely in the output alignment (see this commit for details)

ViralMSA v1.1.11

• Fixed version number (messed with updating)

ViralMSA v1.1.10

• Updated SARS-CoV-2 reference

ViralMSA v1.0.9

• Fixed missing open mode if given a reference genome file (thanks, thanhleviet!)

ViralMSA v1.0.8

• Refactored code and made some optimizations for speed

ViralMSA v1.0.7

• Slight changes to how Minimap2 is called (omits secondary hits)
• Created Dockerfile (all versions starting with 1.0.7 will have Docker images on DockerHub)

ViralMSA v1.0.6

• Added helpful message if reference genome download fails
• Added ViralMSA version number to -h/--help output
• Updated error message if not all sequences appeared in the output
  • Before, I only suggested trying a different aligner
  • It could also be if the reference genome selection is faulty

ViralMSA v1.0.5

• Added ability to specify a local reference genome file rather than a GenBank accession number or virus name, also using -r/--reference