PRALINE sequence alignment toolkit
Project description
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; 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
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
PRALINE is also available on PyPI. You can install it with the following command:
pip install praline
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