ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments

Bioinformatics
Matthias WolfT Müller

Abstract

The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction. For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments-using PNJ with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal also with protein sequences.

References

Sep 1, 1994·Molecular Phylogenetics and Evolution·M Schöniger, A von Haeseler
Dec 11, 1999·Nucleic Acids Research·D L WheelerB A Rapp
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T Müller, M Vingron
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Nov 15, 2006·BMC Bioinformatics·Philipp N SeibelMatthias Wolf
Oct 16, 2007·Nucleic Acids Research·Christian SeligJörg Schultz

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Citations

Aug 8, 2009·Nucleic Acids Research·Roland SchwarzTobias Müller
Nov 19, 2009·Nucleic Acids Research·Christian KoetschanJörg Schultz
Nov 27, 2010·BMC Research Notes·Benjamin Merget, Matthias Wolf
Mar 22, 2012·Journal of Visualized Experiments : JoVE·Benjamin MergetMatthias Wolf
Mar 1, 2012·Molecular Phylogenetics and Evolution·Christian KoetschanJörg Schultz
Apr 27, 2010·Molecular Phylogenetics and Evolution·Daniele SalviPaolo Mariottini
Jun 3, 2009·Molecular Phylogenetics and Evolution·Jörg Schultz, Matthias Wolf
Nov 26, 2008·Gene·Alexander KellerMatthias Wolf
Aug 8, 2009·Molecular Phylogenetics and Evolution·Michael W RuhlTracie M Jenkins
Mar 15, 2015·Trends in Genetics : TIG·Matthias Wolf
Aug 1, 2012·Molecular Phylogenetics and Evolution·Daniele Salvi, Paolo Mariottini
Jul 9, 2013·Toxicon : Official Journal of the International Society on Toxinology·Anita MalhotraRoger S Thorpe
Jun 24, 2014·Saudi Journal of Biological Sciences·M Ajmal AliJoongku Lee

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