ARELIA is a python script that efficiently calculates residue and column reliability scores for given multiple sequence alignments, and masks the alignments based on the reliability scores. Currently, only amino acid alignments are supported.
- A free web server: http://arelia-web.appspot.com/
ARELIA is cross-platform software if the following dependency is satisfied.
Python 2.7 or higher(available at https://www.python.org/).Numpy 1.6 or higher(available at http://www.numpy.org/).
Download arelia.py somewhere in your PATH, and make arelia.py executable. For example, on UNIX-like systems:
chmod +x /path/to/your/arelia.py
Check ARELIA by printing its help message.
arelia.py -h
Or just use it with python command.
python /path/to/your/arelia.py -h
Get a residue-masked MSA.
arelia.py MSA_FILE_IN > MSA_FILE_OUT
or
arelia.py MSA_FILE_IN -msa_res MSA_FILE_OUT
Get a column-masked MSA.
arelia.py MSA_FILE_IN -msa_col MSA_FILE_OUT
Get a residue-masked MSA and residue reliability scores.
arelia.py MSA_FILE_IN -msa_res MSA_FILE_OUT -scr_res SCORE_FILE_OUT
Process all MSA files in a directory recursively.
arelia.py MSA_DIR_IN -msa_res MSA_DIR_OUT -scr_res SCORE_DIR_OUT
Set a gap penalty, window sizes, and cutoff (residues with scores < cutoff will be masked).
arelia.py MSA_FILE_IN -msa_res MSA_FILE_OUT -gap -5.0 -W 5 10 15 30 -cutoff 0.3
Set input and output MSA formats.
arelia.py MSA_DIR_IN -msa_res MSA_DIR_OUT -infmt fasta -outfmt phylip