Click here to see the workflow!
ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.
If you found clipkit useful, please cite ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. Steenwyk et al. 2020, PLoS Biology. doi: 10.1371/journal.pbio.3001007.
Herein, we describe the various trimming modes implemented in ClipKIT. If you are unsure which is appropriate for you, we recommend using the default smart-gap trimming mode.
ClipKIT can be run with eight different modes, which are specified with the -m/–mode argument. Default: ‘smart-gap’
- smart-gap: dynamic determination of gaps threshold
- gappy: trim all sites that are above a threshold of gappyness (default: 0.9)
- kpic: keep only parismony 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