This is the command plotcone that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
plotcon - Plot conservation of a sequence alignment
SYNOPSIS
plotcon -sequences seqset [-scorefile matrix] -winsize integer -graph xygraph
plotcon -help
DESCRIPTION
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).
OPTIONS
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
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