Clean up large gappy multiple sequence alignments.
Project description
GapClean (v1.0.1)
Written by Aarya Venkat, PhD
Description:
GapClean takes a gappy multiple sequence alignment and removes columns with gaps at a
specified threshold value to produce a "cleaner" and easier to visualize sequence alignment.
Can also be used to remove gaps in an alignment relative to a seed sequence to assess site-wise mutational information.
Usage: gapclean [options]
-i Input file (Required)
-o Output file (Required)
-t Threshold value (Optional) Cannot be used with seed argument
-s Seed index (Optional) Cannot be used with threshold argument
-h Display this help message
Example: gapclean -i input.fa -o output.fa -t 75 Removes column from alignment when >75 percent of the column are gaps
Example: gapclean -i input.fa -o output.fa -s 0 Takes first sequence as the seed and removes gaps relative to seed.
INSTALLATION:
-
pip install gapclean
-
Thank Gappy for his service. He is a retired detective.
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