This program is for simple sequence-based clustering of short (aligned) peptide sequences. First, a pairwise distance
matrix is generated from the peptides. This distance matrix is then used to generate a tree using a distance method
such as Neighbour-Joining or UPGMA.
Default distances are amino acid property differences loaded from an amino acid property matrix file.
Version 1.5.0 incorporates a new peptide alignment mode to deal with unaligned peptides. This is controlled by the
peptalign=T/F/X option, which is set to True by default. If given a regular expression, this will be used to guide
the alignment. Otherwise, the longest peptides will be used as a guide and the minimum number of gaps added to
shorter peptides. Pairwise peptide distance measures are used to assess different variants, starting with amino acid
properties, then simple sequence identity (if ties) and finally PAM distances. One of the latter can be set as
the priority using
peptdis=X. Peptide alignment assumes that peptides have termini (^ & $) or flanking wildcards
added. If not, set
peptides=LIST : These can be entered as a list or file. Lines following '#' or '>' ignored [
aaprop=FILE : File of amino acid properties [
aadis=FILE : Alternative amino acid distance matrix [
peptalign=T/F/X : Align peptides. Will use as guide regular expression, else T/True for regex-free alignment. 
termini=T/F : Whether peptides for alignment have termini (^ & $) or X flanking regex match [
maxgapvar=X : Maximum number of consecutive gaps to allow for peptide alignment without Regex guide [
maxgapx=X : Maximum total number of gaps to allow for peptide alignment without Regex guide [
peptdis=X : Method for generating pairwise peptide distances (id/prop/pam) [
peptcluster=X : Clustering mode (upgma/wpgma/neighbor) [
savedis=FILE : Output distance matrix to file [
outmatrix=X : Type for output matrix - tdt / csv / mysql / phylip / png [
savetree=FILE : Save generated tree as FILE [
treeformats=LIST: List of output formats for generated trees (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) [
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation.
# 1.0 - Initial working version.
# 1.1 - Modified output a little.
# 1.2 - CGI Output tuple.
# 1.3 - PAM clustering and WPGMA.
# 1.4 - Bug fixes for end of sequence characters and different length peptides.
# 1.5.0 - Added peptalign=T/F/X function for aligning peptides using regex or minimal gap addition. Added REST.
# 1.5.1 - Updated REST output. Removed peptide redundancy.
# 1.5.2 - Improved clarity of warning message.
# 1.5.3 - Added catching of splitPattern() error during alignment.
PeptCluster REST Output formats
for general options. Run with
to get full server output as text or
for more user-friendly formatted output. Individual outputs can be identified/parsed using
= original input peptides
= aligned peptides
= peptide distance matrix
= peptide tree(s), where X is nsf/nwk/text/png/svg (
made by default.)