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Next-generation PRALINE sequence alignment program.
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PRALINE 2, a reimplementation of the PSI-PRALINE multiple sequence alignment program.


  • Progressive multiple sequence alignment
  • Tree generation through hierarchical clustering and on-the-fly (PRALINE-style)
  • Profile-profile pairwise alignment
  • Affine and linear gap penalties supported; arbitrary gap penalties supported w/ reduced speed
  • Semi-global, global alignment for the MSA merge step
  • Local, global and semi-global preprofile generation
  • Improved preprofile sampling through PSI-BLAST search (requires local installation of NCBI BLAST+)
  • Nucleotide and amino acid alphabets supported out of the box
  • Easy to extend to with arbitrary alphabets (e.g. secondary sequence)
  • Packaged with common substitution matrices (BLOSUM), can be provided to the program.

Coming soon

  • HMM-like gap penalties per position
  • Heuristics to speed up tree building for large numbers of sequences
  • Better multithreading for improved scaling on many-core systems

Installing PRALINE 2


  • Python 2.7 / Python 3.6 (earlier 3.x versions may also work, but have not been tested)
  • A C compiler (C99 support required)
  • NCBI BLAST+ (optional, for homology searching using PSI-BLAST)


You can install PRALINE 2 by cloning this repository and running (in a shell):

python install

PRALINE 2 is also available on PyPI. You can install it with the following command:

pip install praline-aln

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