Biotite 0.29.0

Changelog

Additions

• Extended functionalities for homology searches
  • Added application.tantan.TantanApp for sequence repeat masking with
    Tantan
  • sequence.align.KmerAlphabet and sequence.align.KmerTable support spaced
    k-mers
  • Added sequence.align.local_gapped() and sequence.align.local_ungapped()
    for aligning sequences locally with X-drop heuristic
  • Added EValueEstimator for calculation of expect values (E-values)
    from alignment scores
  • Increased performance of sequence.LetterAlphabet.extends()
• Added sequence.SequenceProfile for representing sequence profiles by means
  of a symbol frequency table
  • sequence.SequenceProfile.from_alignment() creates a profile from an
    alignment
  • sequence.SequenceProfile.to_consenus() creates a consensus sequence
• Increased performance of sequence.align.get_codes() and
  sequence.align.get_symbols()
• Bonds can be read from and written to CONECT records in
  structure.io.pdb.PDBFile (#329)

Changes

• Documentation now uses sphinxcontrib-bibtex for citations
  • Citations include DOI with link to publication

Fixes

• Fixed protein color schemes for sequences containing 'X' or '*' (#322)
• sequence.graphics,plot_nucleotide_secondary_structure() is now able to set
  the color of symbols (#333)