prettyplot draws a plot of the input sequence alignment. The sequences are rendered in pretty formatting on the specified graphics device. Drawing options control the appearance of the image, such as boxes, colour and shading for highlighting conserved regions.
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For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used.
A consesnsus sequence is calculated for the alignment and individual sequences compared to the consensus using the specified comparison matrix file. The default matrix for protein sequences is EBLOSUM62 and for nucleotide sequences is EDNAFULL. The drawing options render conserved sites and regions identified from the comparisons. For example, residues in a sequence are classed as "identical", "similar" or "other" to the consensus depending on user-specified thresholds of sequence similarity (-pair option). Residues in each class are rendered red, green and black by default (this can be changed).
There are other more general drawing options, for example, controlling the number of residues displayed per line, background shading and whether to display sequence names or not.
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.