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PLOTCON(1e) EMBOSS Manual for Debian PLOTCON(1e)


plotcon - Plot conservation of a sequence alignment


plotcon -sequences seqset [-scorefile matrix] -winsize integer -graph xygraph

plotcon -help


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


Input section

-sequences seqset

File containing a sequence alignment

-scorefile 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.

Required section

-winsize integer

Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be. Default value: 4

Output section

-graph xygraph


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


plotcon is fully documented via the tfm(1) system.


Debian Med Packaging Team <>

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.

05/11/2012 EMBOSS 6.4.0