1. The GUIDANCE web server: estimation of confidence scores for individual alignment positions or individual residues, and filtering or masking of these unreliable positions to reduce errors in downstream analyses such as positive selection inference (dN/dS methods).

2. The HomeBase web server: a searchable collection of homing endonucleases and their predicted target sequences for gene targeting applications.

3. Phylogeny reconstruction: improved accuracy of pairwise distance estimation for neighbor joining and other distance-based phylogeny reconstruction methods - available as part of the SEMPHY package.