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c5shen / WITCH

WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.
GNU General Public License v3.0
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Improved merge code #7

Closed c5shen closed 12 months ago

c5shen commented 12 months ago

Improved query alignment code:

  1. Added option to use WITCH-ng's way to do the query alignment (enabled as default)
  2. Progress bar (tqdm package) for tracking progress
  3. Checkpoint system for weight calculation
  4. Checkpoint system for query alignments. Now user can resume from any point during the WITCH query alignment phase

TODO:

  1. Checkpoint system for backbone construction. That is
    • backbone alignment and tree estimation
    • backbone decomposition and HMMBuild on subsets
    • HMMSearches between queries and all HMMs
c5shen commented 12 months ago

Approved by myself