Advanced Usage

This section describes the various features and options of ClipKIT.


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

# smart-gap-based trimming
clipkit <input>
clipkit -m smart-gap

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

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

# kpic- and smart-gap-based trimming
clipkit <input> -m kpic-smart-gap

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

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

# kpi- and smart-gap-based trimming
clipkit <input> -m kpi-smart-gap

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

Sequence Type

Specifies the type of sequences in the input file. The default is auto-detection of sequence type. Valid options include aa or nt for amino acids and nucleotides. This argument is case insensitive. This matters for what characters are considered gaps. For amino acids, -, ?, *, and X are considered gaps. For nucleotide sequences, the same characters are considered gaps as well as N.

clipkit <input> -s aa

Specify input sequences are amino acids

clipkit <input> -s nt

Specify input sequences are nucleotides

All options

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