CLANS program and manual link:
http://bioinfoserver.rsbs.anu.edu.au/downloads/clans/

program: clans.jar
manual: CLANS_tutorial.pdf

(if you use this program for a publication, please cite:
Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-4.)

CLANS-save-files for the sequence-similarity maps depicted in Figures 3-9 and the Hox15, NOB-1 and EGL-5 analysis are available at (these are bigger files than the sequence files, but provide pre-clustered and labelled maps):
http://bioinfoserver.rsbs.anu.edu.au/downloads/hox_classification/

to open the CLANS save files:
- download the Clans program and CLANS-save-files of interest to a chosen directory
- open a terminal / command line (see tutorial)
- go to the directory in which the clans.jar and Clans-save-files are located
- type "java -jar -Xmx3000m clans.jar filename"
(for bigger files you may need up to 12 GB of RAM, in that case replace the 3000 with a 12000 in the -Xmx setting)

Alignment files can be viewed with AlnEdit
http://bioinfoserver.rsbs.anu.edu.au/programs/alnedit/