Protocol // Sequences
ClipKIT
Trimming sequence alignments with smart, parsimony-informed gap removal.
Installation
Create a conda environment:
conda create -n Clipkit_envconda activate Clipkit_envInstall:
conda install bioconda::clipkitRun
clipkit <input> -m gappy -g 0.5
info
Your output will be generated with the extension .clipkit
Other -m mode options:
| Mode | Description |
|---|---|
| smart-gap | dynamic determination of gaps threshold |
| gappy | trim all sites that are above a threshold of gappyness (default: 0.9) |
| kpic | keep only parsimony informative and constant sites |
| kpic-smart-gap | a combination of kpic- and smart-gap-based trimming |
| kpic-gappy | a combination of kpic- and gappy-based trimming |
| kpi | keep only parsimony informative sites |
| kpi-smart-gap | a combination of kpi- and smart-gap-based trimming |
| kpi-gappy | a combination of kpi- and gappy-based trimming |