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CHANGELOG.md

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  • Version 4.3.7:
    • Clean up run-sepp.sh to expose more options
    • Beginning steps for building more robust builds
  • Version 4.3.6:
    • raise a ValueError if names of fragments to be inserted contain whitespace characters ' ' or '\t'.
  • Version 4.3.5:
    • raise a ValueError if names of fragments to be inserted collide with names of reference sequences.
  • Version 4.3.4:
    • Cleaning up the default (info) log a bit
  • Version 4.3.3:
    • avoid pipes for hmmsearch to deal with memory issues
    • Increase the default -F to 20000
  • Version 4.3.2: more fixes to UPP
    • added a seed number
    • Fixed PASTA alignment and tree file names
    • degap input files when already aligned
    • avoid checking file names twice
  • Version 4.3.1: fixes to UPP
    • In the absence of fragments, outputs are generated in a consistent fashion
    • PASTA alignment and trees are given a name prefixed by the output prefix naem
  • Version 4.3.0:
    • Added (Uyen Mai) an option -M and -S midpoint to break by midpoint and to stop by diameter
  • Version 4.2.3:
    • Added a hard-coded --groups 10 to the pplacer runs to help with memory
  • Version 4.2.2:
    • Add max chunk size
    • Fix logging messages
    • Fix a bug for the -D option after python 3 transition
    • Changed the pplacer step so that each run is on one fragment chunk (not all fragments), as specified using -F
  • Version 4.2.1:
    • Fixed a bug with run_tipp_tools.py path
  • Version 4.2.0:
    • Major change (trying again): TIPP should not include fragments that are fully unclassified in its profile. Fixed this
  • Version 4.1.0:
    • Reduce verbosity by moving some logs from info to debug
  • Verstion 4.0.1:
    • Small bug fixes in UPP after transition to python3
  • Version 4.0.0
    • Several small bug fixes, including, the location of the config file for TIPP and UPP
    • Major change: TIPP should not include fragments that are fully unclassified in its profile. Fixed this
  • Version 3.2.2:
    • Bug fix: check for info file for SEPP
  • Version 3.2.1:
    • Can now handle internal node names
  • Version 3.2.0:
    • Can now have a contained installation
  • Version 3.1:
    • Bug fix for TIPP for python 3
  • Version 3:0:
    • Moved to python3
  • Version 1.1:
    • Added -d option for directories
    • Bundled all requied software
    • Changed installation so that dependencies are automatically installed
    • Moved to latest pplacer
    • Misc. bug fixes