%0 Journal Article %1 Milne2004 %A Milne, Iain %A Wright, Frank %A Rowe, Glenn %A Marshall, David F %A Husmeier, Dirk %A McGuire, Gràinne %D 2004 %J Bioinformatics (Oxford, England) %K Alignment,Sequence Alignment: Analysis, Automated,Phylogeny,Programming Computer DNA,Sequence DNA: Expression Genetic,Recombination, Genetic: Graphics,Gene Interface Languages,Recombination, Profiling,Gene Profiling: Recognition, Retrieval,Information Retrieval: Storage Systems,Pattern and genetics,Sequence methods,Information methods,Online methods,Sequence methods,Software,User-Computer %N 11 %P 1806--7 %R 10.1093/bioinformatics/bth155 %T TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. %U http://www.ncbi.nlm.nih.gov/pubmed/14988107 %V 20 %X SUMMARY: TOPALi is a new Java graphical analysis application that allows the user to identify recombinant sequences within a DNA multiple alignment (either automatically or via manual investigation). TOPALi allows a choice of three statistical methods to predict the positions of breakpoints due to past recombination. The breakpoint predictions are then used to identify putative recombinant sequences and their relationships to other sequences. In addition to its sophisticated interface, TOPALi can import many sequence formats, estimate and display phylogenetic trees and allow interactive analysis and/or automatic HTML report generation. AVAILABILITY: TOPALi is freely available from http://www.bioss.ac.uk/software.html

@article{Milne2004, abstract = {SUMMARY: TOPALi is a new Java graphical analysis application that allows the user to identify recombinant sequences within a DNA multiple alignment (either automatically or via manual investigation). TOPALi allows a choice of three statistical methods to predict the positions of breakpoints due to past recombination. The breakpoint predictions are then used to identify putative recombinant sequences and their relationships to other sequences. In addition to its sophisticated interface, TOPALi can import many sequence formats, estimate and display phylogenetic trees and allow interactive analysis and/or automatic HTML report generation. AVAILABILITY: TOPALi is freely available from http://www.bioss.ac.uk/software.html}, added-at = {2011-03-28T19:20:19.000+0200}, author = {Milne, Iain and Wright, Frank and Rowe, Glenn and Marshall, David F and Husmeier, Dirk and McGuire, Gr\`{a}inne}, biburl = {https://www.bibsonomy.org/bibtex/25e7078ae7a5b1686b74c096f7b273366/dunarel}, doi = {10.1093/bioinformatics/bth155}, file = {:/data/PROJET_THESE/Q_FUNC_METHODS/Milne et al._2004_TOPALi software for automatic identification of recombinant sequences within DNA multiple alignments.pdf:PDF}, interhash = {6c3bd435d9c2fc8ecf8bbfa74d8a8cf3}, intrahash = {5e7078ae7a5b1686b74c096f7b273366}, issn = {1367-4803}, journal = {Bioinformatics (Oxford, England)}, keywords = {Alignment,Sequence Alignment: Analysis, Automated,Phylogeny,Programming Computer DNA,Sequence DNA: Expression Genetic,Recombination, Genetic: Graphics,Gene Interface Languages,Recombination, Profiling,Gene Profiling: Recognition, Retrieval,Information Retrieval: Storage Systems,Pattern and genetics,Sequence methods,Information methods,Online methods,Sequence methods,Software,User-Computer}, month = jul, number = 11, owner = {root}, pages = {1806--7}, pmid = {14988107}, timestamp = {2011-03-28T19:20:21.000+0200}, title = {{TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14988107}, volume = 20, year = 2004 }