dotmatcher(1) Draw a threshold dotplot of two sequences


dotmatcher -asequence sequence -bsequence sequence [-matrixfile matrix] [-windowsize integer] [-threshold integer] -stretch toggle -graph graph -xygraph xygraph
dotmatcher -help



is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Alignment:Dot plots" command group(s).


Input section

-asequence sequence

-bsequence sequence

-matrixfile matrix

This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.

Additional section

-windowsize integer

Default value: 10

-threshold integer

Default value: 23

Output section

-stretch toggle

Display a non-proportional graph Default value: N

-graph graph

-xygraph xygraph


Bugs can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.


This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.