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