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PMID: 20439312 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

ALTER: program-oriented conversion of DNA and protein alignments.

Nucleic acids research ·Vol. 38 ·No. Web Server issue ·2010-07-00 ·Pages W14-8

Glez-Peña D, Gómez-Blanco D, Reboiro-Jato M, Fdez-Riverola F, Posada D

Abstract

ALTER is an open web-based tool to transform between different multiple sequence alignment formats. The originality of ALTER lies in the fact that it focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. In addition, ALTER is capable of identify and remove identical sequences during the transformation process. Besides its user-friendly environment, ALTER allows access to its functionalities in a programmatic way through a Representational State Transfer web service. ALTER's front-end and its API are freely available at http://sing.ei.uvigo.es/ALTER/ and http://sing.ei.uvigo.es/ALTER/api/, respectively.

MeSH Terms
Internet Sequence Alignment/methods Sequence Analysis, DNA Sequence Analysis, Protein Software
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Glez-Peña Daniel
Departamento de Informática, Universidad de Vigo, 32004 Ourense, Spain.
Gómez-Blanco Daniel
Reboiro-Jato Miguel
Fdez-Riverola Florentino
Posada David
References (22)
22 references, click to expand
  1. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
    Mol Biol Evol. 2000 Apr;17(4):540-52 PMID: 10742046
  2. Clustal W and Clustal X version 2.0.
    Bioinformatics. 2007 Nov 1;23(21):2947-8 PMID: 17846036
  3. Biopython: freely available Python tools for computational molecular biology and bioinformatics.
    Bioinformatics. 2009 Jun 1;25(11):1422-3 PMID: 19304878
  4. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.
    Bioinformatics. 2009 Jun 1;25(11):1451-2 PMID: 19346325
  5. PAML 4: phylogenetic analysis by maximum likelihood.
    Mol Biol Evol. 2007 Aug;24(8):1586-91 PMID: 17483113
  6. ProtTest: selection of best-fit models of protein evolution.
    Bioinformatics. 2005 May 1;21(9):2104-5 PMID: 15647292
  7. Upcoming challenges for multiple sequence alignment methods in the high-throughput era.
    Bioinformatics. 2009 Oct 1;25(19):2455-65 PMID: 19648142
  8. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
    Syst Biol. 2003 Oct;52(5):696-704 PMID: 14530136
  9. MrBayes 3: Bayesian phylogenetic inference under mixed models.
    Bioinformatics. 2003 Aug 12;19(12):1572-4 PMID: 12912839
  10. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
    Bioinformatics. 2006 Nov 1;22(21):2688-90 PMID: 16928733
  11. TCS: a computer program to estimate gene genealogies.
    Mol Ecol. 2000 Oct;9(10):1657-9 PMID: 11050560
  12. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  13. MAFFT version 5: improvement in accuracy of multiple sequence alignment.
    Nucleic Acids Res. 2005 Jan 20;33(2):511-8 PMID: 15661851
  14. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
    Mol Biol Evol. 2010 Feb;27(2):221-4 PMID: 19854763
  15. T-Coffee: A novel method for fast and accurate multiple sequence alignment.
    J Mol Biol. 2000 Sep 8;302(1):205-17 PMID: 10964570
  16. jModelTest: phylogenetic model averaging.
    Mol Biol Evol. 2008 Jul;25(7):1253-6 PMID: 18397919
  17. The Bioperl toolkit: Perl modules for the life sciences.
    Genome Res. 2002 Oct;12(10):1611-8 PMID: 12368254
  18. ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res. 2005 Feb;15(2):330-40 PMID: 15687296
  19. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics. 2004 Aug 19;5:113 PMID: 15318951
  20. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
    Mol Biol Evol. 2007 Aug;24(8):1596-9 PMID: 17488738
  21. SplitsTree: analyzing and visualizing evolutionary data.
    Bioinformatics. 1998;14(1):68-73 PMID: 9520503
  22. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
    Bioinformatics. 2009 Aug 1;25(15):1972-3 PMID: 19505945
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkq321
Published
2010-07-00
Epub
2010-00-03
Pages
W14-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2896128
Subset
IM
Grants
European Research Council · 203161 · International
External Links
PubMed source DOI: 10.1093/nar/gkq321 PMC Full Text View journal details
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