/arelia

Reliability Scoring and Masking of Multiple Sequence Alignments

Primary LanguagePythonApache License 2.0Apache-2.0

ARELIA

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.

Installation

ARELIA is cross-platform software if the following dependency is satisfied.

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

Examples

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