Advanced Usage
This section describes the various features and options of ClipKIT.
Modes
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
c3: remove third codon position from alignment
cst: custom site trimming (remove sites specified by the user)
# 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
# remove third codon position
clipkit <input> -m c3
# conduct site-specific trimming
clipkit <input> -m cst -a <auxiliary file>
Output
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>
Log
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
Complementary
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’
Codon
Trims codon-based alignments. If one position in a codon should be trimmed, the whole codon will be trimmed. To conduct codon-based trimming, use the -co/\-\-codon argument.
clipkit <input> --codon
# or
clipkit <input> --co
Custom site trimming (cst mode)
Custom site trimming specified using a tab-delimited text file specified using the -a argument.
clipkit <input> -m cst -a <auxiliary_file>
The auxiliary_file is a two column tab-delimited file wherein the first column is the site (starting at 1) and the second column specifies if the site should be kept or trimmed using the strings “keep” or “trim”.
cat auxiliary_file.txt
1 keep
2 trim
3 keep
4 keep
5 keep
6 keep
Alternatively, users can specify sites that are only kept or trimmed using the auxiliary_file. For example, the following would be equivalent to the auxiliary file described above.
cat auxiliary_file.txt
2 trim
Similarly, the following would conduct the trimming, wherein the second site is removed but all others are kept.
cat auxiliary_file.txt
1 keep
3 keep
4 keep
5 keep
6 keep
Gaps
Positions with gappyness greater than threshold will be trimmed. Must be between 0 and 1. (Default: 0.9). This argument is ignored when using the kpi and kpic mdoes of trimming as well as an iteration of trimming that uses smart-gap.
To specify a gaps threshold, use the -g/\-\-gaps argument.
clipkit <input> --gaps 0.4
# or
clipkit <input> --g 0.4
Gap Characters
Specifies gap characters used in the input file. For example, “NnXx-?” would specify that “N”, “n”, “X”, “x”, “-”, and “?” are gap characters. Note, the first gap character cannot be “-” because the parser will interpret the gaps list as a new argument.
clipkit <input> -gc NnXx-?
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
Ends only
For a given trimming mode, specifies if only sites at the end of an alignment should be trimmed. For example, if the sites that should be trimmed include [0, 1, 2, 4, 5, 6, 14, 15, 16] for smart-gap mode and an alignment of length 16, adding the ends_only mode will result in [0, 1, 2, 14, 15, 16] being the sites that will be trimmed. Specify this argument with -eo, --ends_only.
clipkit <input> -eo
# or
clipkit <input> --ends_only
All options
*Acceptable file formats include: fasta, clustal, maf, mauve, phylip, phylip-sequential, phylip-relaxed, stockholm