v1.3.0

• Update muscle dependency to version 5 - breaking: v3 is no longer supported (#48)

Full Changelog: v1.2.1...v1.3.0

Version 1.2.1

• Fix issue in GUI if no proteome is provided (#50)

Version 1.2.0

• Add parameter --genome with translation via prodigal (#15)
• Update and improve documentation (#19, #35, #38, #44)
• Make GUI independent of working directory (#33)
• Switch CI from Travis to GitHub Actions (#45)

Version 1.1.0

• Breaking: the default aa substitution model for RAxML changed from WAG to AUTO.
  This has an impact on performance (it is faster to set this parameter to a fixed value).
  To get the same behaviour as in earlier versions pass --raxml-aa-substitution-model=WAG
• Add parameter --raxml-aa-substitution-model (#29)
• Add HMMs of UBCG (#25)

Version 1.0.10

• Fix GUI, add scrollbar (#23)
• Add parameter --raxml-args (#22)

Version 1.0.9

• Add parameters --min-proteomes and --all-proteomes (#21)

Version 1.0.8

• Set default bootstraps to 100
• Add description for reproduction of results in paper

Version 1.0.7

• Add logo to GUI

Version 1.0.6

• Improve layout (avoid errors with large text fields)
• Update jar file

Version 1.0.5

• Add advanced settings and external programs to GUI
• Add GUI screenshots to README
• Finish GUI layout
• Fix outdir bug (manually entered text was ignored)
• Update documentation in README
• Improve layout of GUI (proteomes panel)