# GapClean (v1.0.2)
###### Written by Aarya Venkat, PhD
<img src="gapclean.png" width="350">
#### 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.
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"description": "# GapClean (v1.0.2) \n###### Written by Aarya Venkat, PhD\n<img src=\"gapclean.png\" width=\"350\">\n\n#### Description: \nGapClean takes a gappy multiple sequence alignment and removes columns with gaps at a \nspecified threshold value to produce a \"cleaner\" and easier to visualize sequence alignment.\n\nCan also be used to remove gaps in an alignment relative to a seed sequence to assess site-wise mutational\ninformation. \n\n#### Usage: gapclean [options]\n\n `-i` Input file (Required)\n\n `-o` Output file (Required)\n\n `-t` Threshold value (Optional) Cannot be used with seed argument\n\n `-s` Seed index (Optional) Cannot be used with threshold argument\n\n `-h` Display this help message\n\n\n##### Example: `gapclean -i input.fa -o output.fa -t 75` \nRemoves column from alignment when >75 percent of the column are gaps \n\n##### Example: `gapclean -i input.fa -o output.fa -s 0` \nTakes first sequence as the seed and removes gaps relative to seed.\n\n \n \n## INSTALLATION:\n\n1. `pip install gapclean`\n\n2. Thank Gappy for his service. He is a retired detective.\n",
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