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Nav Tome (wip)

For navigating the Tomes of biology: genomes, proteomes etc... Currently supports fasta and genbank files

Create a virtual environment with python 3.7 or newer. Virtualenv/Pip is recommended over Conda as there are some issues with Qt and its dependencies.

To setup, open your preferred terminal and type:

pip install -r src/main/python/requirements.txt

If you're on windows, add this as well:

pip install -r src/main/python/requirementsWindows.txt

Then:

fbs run

Contains:

  • a basic web browser to download data from NCBI
  • a parser for the various file types to extract sequence data
  • basic machine learning algorithms
  • distance matrices
  • translation tables
  • naive backtranslation
  • ngrams, trigrams, nucleotide and peptide distribution
  • many sequence similarity calculations
    • cosine
    • levenshtein
    • least common sequence/substrings
    • tversky
    • zlib