Advanced Usage

This section describes the various features and options of ClipKIT.

Modes
Output
Log
Complementary
Codon
Custom site trimming (cst mode)
Gaps
Gap Characters
Sequence Type
All options

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

     keep
     trim
     keep
     keep
     keep
     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

     keep
     keep
     keep
     keep
     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

All options

Option	Usage and meaning
-h/\-\-help	Print help message
-v/\-\-version	Print software version
-m/\-\-mode	Specify trimming mode (default: smart-gap)
-o/\-\-output	Specify output file name
-g/\-\-gaps	Specify gappyness threshold (between 0 and 1). Default: 0.9
-gc/\-\-gap_characters	Specifies gap characters used in input file (AAs: Xx-?; NTs: XxNn-?
-co/\-\-codon	Codon codon-based trimming. Default: off
-s/\-\-sequence	Specifies sequence type of input file. Default: auto-detect
-if/\-\-input_file_format	Specify input file format. Default: auto-detect*
-of/\-\-output_file_format	Specify output file format. Default: input file type*
-l/\-\-log	Create a log file. Default: off
-c/\-\-complementary	Create a complementary alignment file. Default: off
-a/\-\-auxiliary_file	Auxiliary file. Currently used for specifying sites to trim in cst mode

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