Literature DB >> 15201185

QuickJoin--fast neighbour-joining tree reconstruction.

Thomas Mailund1, Christian N S Pedersen.   

Abstract

We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm-while still constructing the same tree as the original neighbour-joining algorithm-making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.

Mesh：

Year:  2004        PMID： 15201185     DOI： 10.1093/bioinformatics/bth359

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


  8 in total

1.  Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

Authors:  Jason Evans; Luke Sheneman; James Foster
Journal:  J Mol Evol       Date:  2006-04-28       Impact factor: 2.395

2.  The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Authors:  Shibu Yooseph; Granger Sutton; Douglas B Rusch; Aaron L Halpern; Shannon J Williamson; Karin Remington; Jonathan A Eisen; Karla B Heidelberg; Gerard Manning; Weizhong Li; Lukasz Jaroszewski; Piotr Cieplak; Christopher S Miller; Huiying Li; Susan T Mashiyama; Marcin P Joachimiak; Christopher van Belle; John-Marc Chandonia; David A Soergel; Yufeng Zhai; Kannan Natarajan; Shaun Lee; Benjamin J Raphael; Vineet Bafna; Robert Friedman; Steven E Brenner; Adam Godzik; David Eisenberg; Jack E Dixon; Susan S Taylor; Robert L Strausberg; Marvin Frazier; J Craig Venter
Journal:  PLoS Biol       Date:  2007-03       Impact factor: 8.029

3.  Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.

Authors:  Ioannis Michalopoulos; Georgios A Pavlopoulos; Apostolos Malatras; Alexandros Karelas; Myrto-Areti Kostadima; Reinhard Schneider; Sophia Kossida
Journal:  BMC Res Notes       Date:  2012-06-06

4.  Fastphylo: fast tools for phylogenetics.

Authors:  Mehmood Alam Khan; Isaac Elias; Erik Sjölund; Kristina Nylander; Roman Valls Guimera; Richard Schobesberger; Peter Schmitzberger; Jens Lagergren; Lars Arvestad
Journal:  BMC Bioinformatics       Date:  2013-11-20       Impact factor: 3.169

5.  The essence of NAC gene family to the cultivation of drought-resistant soybean (Glycine max L. Merr.) cultivars.

Authors:  Reem M Hussain; Mohammed Ali; Xing Feng; Xia Li
Journal:  BMC Plant Biol       Date:  2017-02-28       Impact factor: 4.215

6.  Fast NJ-like algorithms to deal with incomplete distance matrices.

Authors:  Alexis Criscuolo; Olivier Gascuel
Journal:  BMC Bioinformatics       Date:  2008-03-26       Impact factor: 3.169

7.  Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis.

Authors:  Farman Ullah; Dinesh Bhattarai; Zhangrui Cheng; Xianwei Liang; Tingxian Deng; Zia Ur Rehman; Hira Sajjad Talpur; Tesfaye Worku; Rahim Dad Brohi; Muhammad Safdar; Muhammad Jamil Ahmad; Mohammad Salim; Momen Khan; Hafiz Ishfaq Ahmad; Shujun Zhang
Journal:  Biomed Res Int       Date:  2018-05-15       Impact factor: 3.411

8.  Live neighbor-joining.

Authors:  Guilherme P Telles; Graziela S Araújo; Maria E M T Walter; Marcelo M Brigido; Nalvo F Almeida
Journal:  BMC Bioinformatics       Date:  2018-05-16       Impact factor: 3.169
  8 in total

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