Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

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

Project details


Release history Release notifications

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for praline-aln, version 1.1.0
Filename, size File type Python version Upload date Hashes
Filename, size praline_aln-1.1.0-cp27-cp27m-macosx_10_14_intel.whl (91.6 kB) File type Wheel Python version cp27 Upload date Hashes View hashes
Filename, size praline_aln-1.1.0-cp36-cp36m-macosx_10_13_x86_64.whl (95.1 kB) File type Wheel Python version cp36 Upload date Hashes View hashes
Filename, size praline-aln-1.1.0.tar.gz (60.7 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page