Affiliation: Wellcome Trust Genome Campus
- MATLIGN: a motif clustering, comparison and matching toolMatti Kankainen
Institute of Biotechnology, University of Helsinki, Helsinki, Finland
BMC Bioinformatics 8:189. 2007..Efficient post-processing, for example, reduces the redundancy of the motifs predicted and enables them to be annotated...
- An algorithm for progressive multiple alignment of sequences with insertionsAri Löytynoja
European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
Proc Natl Acad Sci U S A 102:10557-62. 2005..Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms...
- Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysisAri Löytynoja
European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Science 320:1632-5. 2008..These results suggest that insertions and sequence turnover are more common than is currently thought and challenge the conventional picture of sequence evolution and mechanisms of functional and structural changes...
- A model of evolution and structure for multiple sequence alignmentAri Löytynoja
EMBL European Bioinformatics Institute, Hinxton, UK
Philos Trans R Soc Lond B Biol Sci 363:3913-9. 2008....
- webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browserAri Löytynoja
EMBL European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
BMC Bioinformatics 11:579. 2010..g. by objectively selecting subsets of alignment sites...
- Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithmAri Löytynoja
EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, UK
Bioinformatics 28:1684-91. 2012..These do not incorporate and use phylogenetic information and are affected by the composition of the reference alignment and the phylogenetic positions of query sequences...
- Alignment methods: strategies, challenges, benchmarking, and comparative overviewAri Löytynoja
European Bioinformatics Institute EMBL, Hinxton, UK
Methods Mol Biol 855:203-35. 2012..As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended...