kPAL provides a command-line analysis toolkit for creating, analysing, and manipulating k-mer profiles. It is implemented in Python.

After following Installation, kPAL can be started by typing:

$ kpal

More information about the available commands and their arguments is printed by adding the -h argument.

For example, to count all 9-mers in a FASTA file, use the count command:

$ kpal count -k 9 example.fasta example.k9

Below, we provide an overview of all functions of kPAL that are available via the command-line interface:

Command Description
count Make a profile from a FASTA file.
merge Merge two profiles.
balance Balance a profile on the frequency of k-mers and their reverse complements.
showbalance Calculate the balance of a profile.
meanstd Show the mean and standard deviation of k-mer frequencies.
distr Calculate the distribution of the frequencies in a profile.
info Print basic statistics on a given profile.
getcount Retrieve the count for a particular k-mer.
positive Only keep counts that are positive in both profiles.
scale Scale profiles such that the total number of k-mer frequencies is equal.
shrink Shrink a profile, effectively reducing k-mer length.
shuffle Randomise a profile.
smooth Smooth two profiles by collapsing sub-profiles.
distance Calculate the distance between two profiles.
matrix Make a pairwise distance matrix for a series of k-mer profiles.
cat Save profiles from several files to one file.

More information about the methods implemented by kPAL can be found in Methodology. Some examples of working with the toolkit are shown in Tutorial.