I was using MatGAT for sequence similarity and identity calculations a while ago. However, recently I noticed running MatGAT on my computer repeatedly failed. MatGAT is a good tool to handle and calculate the homology at one step. I wonder whether there is any similar platform to derive the homology matrix in the form of a table without individually feeding and executing sequence-pairs, such as in Emboss tool (http://www.ebi.ac.uk/Tools/psa/) at EBI?
I suggest that you use Discovery Studio Accelrys - accelrys provides a free Vizualizer that you can download from
http://accelrys.com/products/discovery-studio/visualization-download.php
Have a look at TraMineR. It can compute pairwise dissimilarities up to several thousands of sequences.
http://cran.r-project.org/web/packages/TraMineR/
http://traminer.unige.ch/
If you are working with proteins and have their PDB id's, you can use SuperPose. It generates a difference distance matrix between two sequences.
http://wishart.biology.ualberta.ca/SuperPose/
GABLAM will construct pairwise global % identities and similarities from BLAST results, giving a zero value if there is no BLAST-detectable homology. I'm not sure what your input data is but be careful about using pairwise tools that assume homology if you do not know that your sequences are homologous - at low %identity, you will just be measuring chance similarity.
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