Literature DB >> 19541988

Evolution. Uniting alignments and trees.

Ari Löytynoja1, Nick Goldman.   

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Year:  2009        PMID： 19541988     DOI： 10.1126/science.1175949

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


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  11 in total

Review 1.  The interface of protein structure, protein biophysics, and molecular evolution.

Authors:  David A Liberles; Sarah A Teichmann; Ivet Bahar; Ugo Bastolla; Jesse Bloom; Erich Bornberg-Bauer; Lucy J Colwell; A P Jason de Koning; Nikolay V Dokholyan; Julian Echave; Arne Elofsson; Dietlind L Gerloff; Richard A Goldstein; Johan A Grahnen; Mark T Holder; Clemens Lakner; Nicholas Lartillot; Simon C Lovell; Gavin Naylor; Tina Perica; David D Pollock; Tal Pupko; Lynne Regan; Andrew Roger; Nimrod Rubinstein; Eugene Shakhnovich; Kimmen Sjölander; Shamil Sunyaev; Ashley I Teufel; Jeffrey L Thorne; Joseph W Thornton; Daniel M Weinreich; Simon Whelan
Journal:  Protein Sci       Date:  2012-04-23       Impact factor: 6.725

2.  Detecting Horizontal Gene Transfer between Closely Related Taxa.

Authors:  Orit Adato; Noga Ninyo; Uri Gophna; Sagi Snir
Journal:  PLoS Comput Biol       Date:  2015-10-06       Impact factor: 4.475

3.  Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability.

Authors:  Jia-Ming Chang; Evan W Floden; Javier Herrero; Olivier Gascuel; Paolo Di Tommaso; Cedric Notredame
Journal:  Bioinformatics       Date:  2019-02-06       Impact factor: 6.937

4.  Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.

Authors:  Annamária Tóth; Anton Hausknecht; Irmgard Krisai-Greilhuber; Tamás Papp; Csaba Vágvölgyi; László G Nagy
Journal:  PLoS One       Date:  2013-02-13       Impact factor: 3.240

5.  Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

Authors:  Zheng Wang; R Henrik Nilsson; Francesc Lopez-Giraldez; Wen-ying Zhuang; Yu-cheng Dai; Peter R Johnston; Jeffrey P Townsend
Journal:  PLoS One       Date:  2011-04-21       Impact factor: 3.240

6.  PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.

Authors:  Botond Sipos; Tim Massingham; Gregory E Jordan; Nick Goldman
Journal:  BMC Bioinformatics       Date:  2011-04-19       Impact factor: 3.307

7.  Phylo: a citizen science approach for improving multiple sequence alignment.

Authors:  Alexander Kawrykow; Gary Roumanis; Alfred Kam; Daniel Kwak; Clarence Leung; Chu Wu; Eleyine Zarour; Luis Sarmenta; Mathieu Blanchette; Jérôme Waldispühl
Journal:  PLoS One       Date:  2012-03-07       Impact factor: 3.240

8.  Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.

Authors:  Ari Löytynoja; Albert J Vilella; Nick Goldman
Journal:  Bioinformatics       Date:  2012-04-23       Impact factor: 6.937

9.  Incorrect handling of calibration information in divergence time inference: an example from volcanic islands.

Authors:  Beatriz Mello; Carlos G Schrago
Journal:  Ecol Evol       Date:  2012-03       Impact factor: 2.912

10.  Looking for the Last Universal Common Ancestor (LUCA).

Authors:  Minna Koskela; Arto Annila
Journal:  Genes (Basel)       Date:  2012-01-09       Impact factor: 4.096
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