Skip Navigation


Bioinformatics Advance Access originally published online on November 4, 2008
Bioinformatics 2009 25(1):126-127; doi:10.1093/bioinformatics/btn575
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
25/1/126    most recent
btn575v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Milne, I.
Right arrow Articles by Wright, F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Milne, I.
Right arrow Articles by Wright, F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

Iain Milne 1,*, Dominik Lindner 2, Micha Bayer 1, Dirk Husmeier 3, Gráinne McGuire 3, David F. Marshall 1 and Frank Wright 2

1Scottish Crop Research Institute, 2Biomathematics and Statistics Scotland (BioSS), SCRI, Invergowrie, Dundee DD2 5DA and 3Biomathematics and Statistics Scotland (BioSS), JCMB, The King's Buildings, Edinburgh EH9 3JZ, UK

*To whom correspondence should be addressed.


  Abstract

Summary: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian inference and maximum likelihood (ML) approaches, in addition to recombination detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes.

Availability: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.

Contact: iain.milne{at}scri.ac.uk

Associate Editor: Martin Bishop

Received on August 2, 2008; revised on November 3, 2008; accepted on November 3, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Gen. Virol.Home page
J. G. Olveira, S. Souto, C. P. Dopazo, R. Thiery, J. L. Barja, and I. Bandin
Comparative analysis of both genomic segments of betanodaviruses isolated from epizootic outbreaks in farmed fish species provides evidence for genetic reassortment
J. Gen. Virol., December 1, 2009; 90(12): 2940 - 2951.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, and M. Stanke
jpHMM: Improving the reliability of recombination prediction in HIV-1
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W647 - W651.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.