PRALINE

Reimplementation of the PRALINE multiple sequence alignment program.

Features

• 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
• 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 extensible to arbitrary alphabets (for example 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

Requirements

• 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)

Instructions

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

python setup.py install

A version will be uploaded to PyPI in the near future, which should make PRALINE installable with:

pip install praline