AlnEdit
Tancred Frickey
Originally developed at the Max-Planck-Institute for Developmental Biology Tuebingen
Research School of Biological Sciences
Australian National University, Canberra

The alignment editor is available HERE.

Motivation:
Although a multitude of alignment editors already exist, I was unable to find any that were easy to install (not requiring special libraries), able to color code residues (similar to clustalx), capable of handling LARGE alignments (thousands of sequences) without slowing to a crawl and where sequence alignments could be edited by hand. So, after hours of intensely frustrating installing, deinstalling and fruitless searching, I started developing my own.
NOTE: It still is under development so I'd be happy about any bug-reports or must-have features you encounter.

Program:

Screenshot of the alignment editor and a few features: This is an alignment view of the individual blades of a few 7 bladed WD40 repeat proteins. All uppercase characters are colored, coloring scheme is clustalx Topmost is the 'coloring window'. Here you can select the colors for the individual amino acids. On the left, below, is a selection of profiles calculated for the individual blade alignments. On the right is a view of the individual blade profiles and their comparison. The green bars symbolize the conservation within the profile at each position, blue bars show the congruence between the selected profile (blade 6, highlighted in light red) and the corresponding profile (blade 1-5 + 7). On the bottom is the alignment editor with all uppercase residues colored according to the selected color scheme. Gaps characters, residues or selected groups of both can be added, removed, shifted right or left; in short, alignment editing is done here.