Advanced Usage

This section describes the various features and options of ClipKIT.


ClipKIT can be run with five different modes (gappy, kpic, kpic-gappy, kpi, and kpi-gappy), which are specified with the -m/–mode argument. Default: ‘gappy’

  • gappy: trim all sites that are above a threshold of gappyness (default: 0.9)

  • kpic (alias: medium): keep only parismony informative and constant sites

  • kpic-gappy (alias: medium-gappy): a combination of kpic- and gappy-based trimming

  • kpi (alias: heavy): keep only parsimony informative sites

  • kpi-gappy (alias: heavy-gappy): a combination of kpi- and gappy-based trimming

# gappy-based trimming
clipkit <input>
clipkit <input> -m gappy

# kpic-based trimming
clipkit <input> -m kpic
clipkit <input> -m medium

# kpic- and gappy-based trimming
clipkit <input> -m kpic-gappy
clipkit <input> -m medium-gappy

# kpi-based trimming
clipkit <input> -m kpi
clipkit <input> -m heavy

# kpi- and gappy-based trimming
clipkit <input> -m kpi-gappy
clipkit <input> -m heavy-gappy


By default, output files will have the same name as the input file with the suffix “.clipkit” appended to the name. Users can specify output file names with the -o option.

# specify output
clipkit <input> -o <output>


It can be very useful to have information about the each position in an alignment. For example, this information could be used in alignment diagnostics, fine-tuning of trimming parameters, etc. To create the log file, use the -l/--log option. Using this option will create a four column file with the suffix ‘clipkit.log’. Default: off

  • col1: position in the alignment (starting at 1)

  • col2: reports if site was trimmed or kept (trim or keep, respectively)

  • col3: reports if the site is parsimony informative or not (PI or nPI, respectively)

  • col4: reports the gappyness of the position (number of gaps / entries in alignment)

clipkit <input> -l


Having an alignment of the sequences that were trimmed can be useful for other analyses. To obtain an alignment of the sequences that were trimmed, use the -c/--complementary option.

clipkit <input> -c

Output file with the suffix ‘.clipkit.complementary’

All options


Usage and meaning


Print help message


Print software version


Specify output file name


Specify gappyness threshold (between 0 and 1). Default: 0.9


Specify input file format*. Default: auto-detect


Specify output file format*. Default: input file type


Create a log file. Default: off


Create a complementary alignment file. Default: off

*Acceptable file formats include: fasta, clustal, maf, mauve, phylip, phylip-sequential, phylip-relaxed, stockholm