Literature DB >> 25564672

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Ge Tan1, Manuel Gil2, Ari P Löytynoja3, Nick Goldman4, Christophe Dessimoz5.   

Abstract

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Year:  2015        PMID： 25564672      PMCID： PMC4299236          DOI： 10.1073/pnas.1417526112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  5 in total

Review 1.  Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

Authors:  Stefano Iantorno; Kevin Gori; Nick Goldman; Manuel Gil; Christophe Dessimoz
Journal:  Methods Mol Biol       Date:  2014

2.  Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.

Authors:  Ari Löytynoja; Nick Goldman
Journal:  Science       Date:  2008-06-20       Impact factor: 47.728

3.  Simple chained guide trees give high-quality protein multiple sequence alignments.

Authors:  Kieran Boyce; Fabian Sievers; Desmond G Higgins
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-07       Impact factor: 11.205

4.  Phylogenetic assessment of alignments reveals neglected tree signal in gaps.

Authors:  Christophe Dessimoz; Manuel Gil
Journal:  Genome Biol       Date:  2010-04-06       Impact factor: 13.583

5.  ALF--a simulation framework for genome evolution.

Authors:  Daniel A Dalquen; Maria Anisimova; Gaston H Gonnet; Christophe Dessimoz
Journal:  Mol Biol Evol       Date:  2011-12-08       Impact factor: 16.240
  5 in total
  12 in total

1.  Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments.

Authors:  Kieran Boyce; Fabian Sievers; Desmond G Higgins
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-06       Impact factor: 11.205

2.  Protein multiple sequence alignment benchmarking through secondary structure prediction.

Authors:  Quan Le; Fabian Sievers; Desmond G Higgins
Journal:  Bioinformatics       Date:  2017-05-01       Impact factor: 6.937

3.  Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees.

Authors:  Kazunori D Yamada; Kentaro Tomii; Kazutaka Katoh
Journal:  Bioinformatics       Date:  2016-07-04       Impact factor: 6.937

4.  QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families.

Authors:  Adam Gudyś; Sebastian Deorowicz
Journal:  Sci Rep       Date:  2017-01-31       Impact factor: 4.379

Review 5.  Systematic benchmarking of omics computational tools.

Authors:  Serghei Mangul; Lana S Martin; Brian L Hill; Angela Ka-Mei Lam; Margaret G Distler; Alex Zelikovsky; Eleazar Eskin; Jonathan Flint
Journal:  Nat Commun       Date:  2019-03-27       Impact factor: 14.919

6.  DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.

Authors:  Erik S Wright
Journal:  BMC Bioinformatics       Date:  2015-10-06       Impact factor: 3.169

7.  FAMSA: Fast and accurate multiple sequence alignment of huge protein families.

Authors:  Sebastian Deorowicz; Agnieszka Debudaj-Grabysz; Adam Gudyś
Journal:  Sci Rep       Date:  2016-09-27       Impact factor: 4.379

8.  Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments.

Authors:  Gearóid Fox; Fabian Sievers; Desmond G Higgins
Journal:  Bioinformatics       Date:  2015-11-14       Impact factor: 6.937

9.  Alignment Modulates Ancestral Sequence Reconstruction Accuracy.

Authors:  Ricardo Assunção Vialle; Asif U Tamuri; Nick Goldman
Journal:  Mol Biol Evol       Date:  2018-07-01       Impact factor: 16.240

10.  Progressive multiple sequence alignment with indel evolution.

Authors:  Massimo Maiolo; Xiaolei Zhang; Manuel Gil; Maria Anisimova
Journal:  BMC Bioinformatics       Date:  2018-09-21       Impact factor: 3.169
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