Literature DB >> 15677706

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.

Joachim Friedrich1, Thomas Dandekar, Matthias Wolf, Tobias Müller.   

Abstract

SUMMARY: ProfDist is a user-friendly software package using the profile-neighbor-joining method (PNJ) in inferring phylogenies based on profile distances on DNA or RNA sequences. It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy. AVAILABILITY: A Windows version of ProfDist comes with a graphical user interface and is freely available at http://profdist.bioapps.biozentrum.uni-wuerzburg.de

Mesh：

Year:  2005        PMID： 15677706     DOI： 10.1093/bioinformatics/bti289

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  17 in total

1.  Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2.

Authors:  Mark A Buchheim; Danica M Sutherland; Tina Schleicher; Frank Förster; Matthias Wolf
Journal:  Ann Bot       Date:  2011-10-25       Impact factor: 4.357

2.  Coccomyxa: a dominant planktic alga in two acid lakes of different origin.

Authors:  Dovilė Barcytė; Linda Nedbalová
Journal:  Extremophiles       Date:  2016-12-09       Impact factor: 2.395

3.  Detecting species-site dependencies in large multiple sequence alignments.

Authors:  Roland Schwarz; Philipp N Seibel; Sven Rahmann; Christoph Schoen; Mirja Huenerberg; Clemens Müller-Reible; Thomas Dandekar; Rachel Karchin; Jörg Schultz; Tobias Müller
Journal:  Nucleic Acids Res       Date:  2009-08-06       Impact factor: 16.971

4.  A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data.

Authors:  Benjamin Merget; Matthias Wolf
Journal:  BMC Res Notes       Date:  2010-11-25

5.  Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

Authors:  Alexander Keller; Frank Förster; Tobias Müller; Thomas Dandekar; Jörg Schultz; Matthias Wolf
Journal:  Biol Direct       Date:  2010-01-15       Impact factor: 4.540

6.  Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.

Authors:  Mark A Buchheim; Alexander Keller; Christian Koetschan; Frank Förster; Benjamin Merget; Matthias Wolf
Journal:  PLoS One       Date:  2011-02-10       Impact factor: 3.240

7.  Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae.

Authors:  Danwei Huang; Wilfredo Y Licuanan; Andrew H Baird; Hironobu Fukami
Journal:  BMC Evol Biol       Date:  2011-02-07       Impact factor: 3.260

8.  Evolutionary distances in the twilight zone--a rational kernel approach.

Authors:  Roland F Schwarz; William Fletcher; Frank Förster; Benjamin Merget; Matthias Wolf; Jörg Schultz; Florian Markowetz
Journal:  PLoS One       Date:  2010-12-31       Impact factor: 3.240

9.  ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus ).

Authors:  Martin Wiemers; Alexander Keller; Matthias Wolf
Journal:  BMC Evol Biol       Date:  2009-12-26       Impact factor: 3.260

10.  Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).

Authors:  Nataliya Rybalka; Matthias Wolf; Robert A Andersen; Thomas Friedl
Journal:  BMC Evol Biol       Date:  2013-02-13       Impact factor: 3.260
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