gapclean 1.0.2

Clean up large gappy multiple sequence alignments.

GapClean (v1.0.2)

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:

1. pip install gapclean

2. Thank Gappy for his service. He is a retired detective.