CHANGELOG.md

• Version 4.5.5:
  • Keep backwards compatible with dendropy < 4.5.2
• Version 4.5.4:
  • Slight improvements in logging key information
• Version 4.5.3:
  • Make sure SEPP and HMMER version is outputted to log
  • Update documents to ask users to cite HMMER
• Version 4.5.2:
  • New -M functionality
• Version 4.5.1:
  • fix small issues (broken links, etc.) in 4.5.0
• Version 4.5.0:
  • TIPP has moved to a new repo: https://github.com/TeraTrees/TIPP
• Version 4.4.0:
  • TIPP has moved to TIPP2
• Version 4.3.21:
  • one more small bug fix
• Version 4.3.20:
  • Added --ignore-overlap option to ignore overlap.
• Version 4.3.19:
  • Enable --symfrac from config file
  • Enable config files that overwrite the default values only when provided
• Version 4.3.18:
  • UPP speed improvement for cases with super gappy backbone alignment (more can be done)
  • Slightly better logging
• Version 4.3.17:
  • Attempt to make tests python 3.8 friendly
  • Add UPP test
• Version 4.3.16:
  • Refactor code slightly. Reduces warnings
• Version 4.3.15:
  • some py3.8 changes and some java changes from pgrt
• Version 4.3.14:
  • Added option -R "Nmin Nmax" to specify the range of full length sequences to UPP
• Version 4.3.13:
  • Added backtranslation functionality to UPP for amino acid sequences.
• Version 4.3.12:
  • Added -rt to remove temp files
• Version 4.3.11:
  • Make sure PASTA user options can be passed
• Version 4.3.10:
  • fix issue #70 a bug when hmmsearch fake jobs where not piped
• Version 4.3.9:
  • fix info file path in run_sepp.sh script
• 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