Appnr

Multiple alignment of nucleic acid and protein sequences (graphical interface)

This package offers a GUI interface for the Clustal multiple sequence
alignment program. It provides an integrated environment for performing
multiple sequence- and profile-alignments to analyse the results.
The sequence alignment is displayed in a window on the screen.
A versatile coloring scheme has been incorporated to highlight conserved
features in the alignment. For professional presentations, one should
use the texshade LaTeX package or boxshade.

The pull-down menus at the top of the window allow you to select all the
options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can
select a subset of sequences to be aligned; you can select a sub-range of the
alignment to be realigned and inserted back into the original alignment.

An alignment quality analysis can be performed and low-scoring segments or
exceptional residues can be highlighted.