prettyplot
Function
Description
prettyplot reads in a set of aligned DNA or protein sequences.
It displays them graphically, with conserved regions highlighted in
various ways.
Usage
Command line arguments
Input file format
prettyplot reads any sequence USA.
Output file format
An image of the alignment is displayed on the specified graphics device.
Data files
Prettyplot uses a comparison matrix file to calculate similarity to
the consensus.
For protein sequences EBLOSUM62 is used for the substitution matrix.
For nucleotide sequence, EDNAFULL is used.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It exits with status 0 unless an error is reported.
Known bugs
Portrait mode does not cover the whole page! This is a "feature" in
plplot.
Author(s)
Many features were first implemented in the EGCG program "prettyplot" by
The original suggestions for the PrettyPlot program were from Denis
Duboule and Sigfried Labeit at EMBL. Gert Vriend added the star
marking. Rita Grandori suggested the -NOCOLLISION option.
History
Target users
Comments