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Bioinformatics Advance Access first published online on January 17, 2006
This version published online on January 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl007
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 4, 2005
Revised January 12, 2006
Accepted January 13, 2006

Applications note

Panta rhei (QAlign2): an open graphical environment for sequence analysis

Michael Sammeth 1, Thasso Griebel 1, Felix Tille 1, and Jens Stoye 1 *

1 Genome Informatics, Technical faculty, Bielefeld University, P.O. Box 10 01 31, 33501 Bielefeld, Germany


  Abstract

Motivation: The first version of the graphical multiple sequence alignment environment QAlign has been published in 2003. Heavy response from the molecular-biological user community clearly demonstrated the need for such a platform.

Results: Panta rhei extends QAlign by several features. A workspace allows to administrate multiple projects (i.e., sequence sets). Major redesigns have been performed on the graphical user interface, such that now individualized views can be flexibly designed. A new sequence viewer allows to handle data sets with arbitrarily many and arbitrarily large sequences that may still be edited by guided block moving. In addition to flat file formats (e.g., MSF and FASTA), an XML-based format now exports additional features like the blocks and phylogenetic trees within a project. The interactive tree reconstruction abilities have been extended by more distance-based algorithms (UPGMA, WPGMA, agglomerative clustering) in addition to the already existing Neighbor Joining method. Finally, also the tree viewer has been enhanced by a more convenient zoom and navigation functionality.

Availability: Executables and source code are available under the Apache license at http://gi.cebitec.uni-bielefeld.de/qalign.

Associate Editor: Dmitrij Frishman
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