HoT / Guidance

Multiple Sequence Alignment Quality Scores

We have a new web server that implements both Guidance and HoT/COS, try it out at: http://guidance.tau.ac.il/

To run HoT on your own, download this newest version of HoT tarball: COS_LRM_v2.05.tgz

It contains the HOT/COS perl script and a C++ scoring program.

Please see the README files and let me know if you need help at giddy.landan@gmail.com

The relevant papers are:

Penn O, Privman E, Ashkenazy H, Landan G, Graur D and Pupko T. 2010. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38 Suppl:W23-8

Penn O, Privman E, Landan G, Graur D and Pupko T. 2010. An alignment confidence score capturing robustness to guide-tree uncertainty. Mol. Biol. Evol. 27:1759-67

Landan G and Graur D. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pac. Symp. Biocomput. 2008:15-24.

Landan G and Graur D. 2007. Heads or Tails: a simple reliability check for multiple sequence alignments. Mol. Biol. Evol. 24:1380-3.