[Biopython-dev] Fwd: [raxml] Are all global alignment algorithms and implementations correct?

Peter Cock p.j.a.cock at googlemail.com
Fri Nov 13 10:39:28 UTC 2015

Apparently Bio.pairwise2 can produce suboptimal alignments
and suffers from other constraints:


In particular it seems Flouri et al would like to allow for insertions
that are immediately followed by deletions?


---------- Forwarded message ----------
From: Alexandros Stamatakis <alexandros.stamatakis at gmail.com>
Date: Fri, Nov 13, 2015 at 10:29 AM
Subject: [raxml] Are all global alignment algorithms and
implementations correct?

Dear Users,

Please accept my apologies for slightly abusing our support groups.

I wanted to share this biorxiv preprint with you that addresses some
fundamental problems in the implementations of global pair-wise
sequence alignment algorithms:


Please spread the word, especially to those teaching Bioinformatics courses.

Thanks a lot,


Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson


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