Tan, G., Gil, M., Löytynoja, A. P., Goldman, N. and Dessimoz, C. Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc. Natl. Acad. Sci. USA...
Medlar, Aivelo, and Löytynoja. 2014. Séance: reference-based phylogenetic analysis for 18S rRNA studies. BMC Evol Biol 14, 235. Background: Marker gene studies often use short amplicons spanning one or more hypervariable regions from an...
Löytynoja, A., Vilella, A. J. & Goldman, N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28, 1684–1691 (2012). Motivation: Accurate alignment of large numbers of sequences is demanding and the...
ENCODE Project Consortium et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007). We report the generation and analysis of functional...
Löytynoja, A. & Goldman, N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11, 579 (2010). Background Phylogeny-aware progressive alignment has been found to perform well in phylogenetic alignment benchmarks...
Löytynoja, A. & Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632–1635 (2008). Genetic sequence alignment is the basis of many evolutionary and comparative studies, and errors...
Löytynoja, A. Alignment methods: strategies, challenges, benchmarking, and comparative overview. Methods Mol. Biol. 855, 203–235 (2012). Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters....
Löytynoja, A. & Goldman, N. A model of evolution and structure for multiple sequence alignment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 3913–3919 (2008). We have developed a phylogeny-aware progressive alignment method...
Löytynoja, A. & Goldman, N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. U. S. A. 102, 10557–10562 (2005). Dynamic programming algorithms guarantee to find the optimal alignment...
Löytynoja, A. & Goldman, N. Evolution. Uniting alignments and trees. Science 324, 1528–1529 (2009). Phylogenetic trees depicting the evolutionary relatedness of different species or groups of species are often determined by analyzing the similarities...
Löytynoja, A. Phylogeny-aware alignment with PRANK. Methods Mol. Biol. 1079, 155–170 (2014). Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary and structural homology are not the same and sequence alignments generated...
