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
1 maintainer
Metadata
1 maintainer
Release files for praline-aln 1.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| praline-aln-1.1.0.tar.gz | 60.7 kB | Without provenance | Details for praline-aln-1.1.0.tar.gz |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| praline_aln-1.1.0-cp36-cp36m-macosx_10_13_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | macOS 10.13+ x86-64 | Details for praline_aln-1.1.0-cp36-cp36m-macosx_10_13_x86_64.whl |
| praline_aln-1.1.0-cp27-cp27m-macosx_10_14_intel.whl | CPython 2.7 | CPython 2.7 pymalloc | macOS 10.14+ Intel (x86-64, i386) | Details for praline_aln-1.1.0-cp27-cp27m-macosx_10_14_intel.whl |
Total release size: 247.5 kB
Release files / praline-aln-1.1.0.tar.gz
| Download URL | praline-aln-1.1.0.tar.gz |
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| Size | 60.7 kB |
| Tags | Source |
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Release files / praline_aln-1.1.0-cp36-cp36m-macosx_10_13_x86_64.whl
| Download URL | praline_aln-1.1.0-cp36-cp36m-macosx_10_13_x86_64.whl |
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| Size | 95.1 kB |
| Tags | CPython 3.6 CPython 3.6 pymalloc macOS 10.13+ x86-64 |
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Release files / praline_aln-1.1.0-cp27-cp27m-macosx_10_14_intel.whl
| Download URL | praline_aln-1.1.0-cp27-cp27m-macosx_10_14_intel.whl |
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| Size | 91.6 kB |
| Tags | CPython 2.7 CPython 2.7 pymalloc macOS 10.14+ Intel (x86-64, i386) |
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