webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

By Ari Löytynoja, Nick Goldman. BMC Bioinformatics, 2010

448 citations recorded by the source corpus.

BackgroundPhylogeny-aware progressive alignment has been found to perform well in phylogenetic alignment benchmarks and to produce superior alignments for the inference of selection on codon sequences. Its implementation in the PRANK alignment program package also allows modelling of complex evolutionary processes and inference of posterior probabilities for sequence sites evolving under each distinct scenario, either simultaneously with the alignment of sequences or as a post-processing step for an existing alignment. This has led to software with many advanced features, and users may find it difficult to generate optimal alignments, visualise the full information in their alignment results, or post-process these results, e.g. by objectively selecting subsets of alignment sites.ResultsWe have created a web server called webPRANK that provides an easy-to-use interface to the PRANK phylogeny-aware alignment algorithm. The webPRANK server supports the alignment of DNA, protein and codon sequences as well as protein-translated alignment of cDNAs, and includes built-in structure models for the alignment of genomic sequences. The resulting alignments can be exported in various formats widely used in evolutionary sequence analyses. The webPRANK server also includes a powerful web-based alignment browser for the visualisation and post-processing of the results in the context of a cladogram relating the sequences, allowing (e.g.) removal of alignment columns with low posterior reliability. In addition to de novo alignments, webPRANK can be used for the inference of ancestral sequences with phylogenetically realistic gap patterns, and for the annotation and post-processing of existing alignments. The webPRANK server is freely available on the web at http://tinyurl.com/webprank .ConclusionsThe webPRANK server incorporates phylogeny-aware multiple sequence alignment, visualisation and post-processing in an easy-to-use web interface. It widens the user base of phylogeny-aware multiple sequence alignment and allows the performance of all alignment-related activity for small sequence analysis projects using only a standard web browser.

Subfields: Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/2c94786153ff6bb8fa96f024516d8dca01f337ae

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Citations in the corpus

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages (2019, methodology): “Nucleotide sequences for 79 immunity repressors from L5 clade phages were aligned by codon using webPRANK (51), and a phylogenetic tree was constructed using maximum likelihood in SeaView (50) and annotated using Evolview (52).”
ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016, methodology): “To date, several browser-based protein data visualization tools of varying degrees of sophistication have been developed including Java applet based tools (JalView2 Lite (24), STRAP (25), PFAAT (26)), resource specific tools (PDB viewers (27,28), Pfam (3), webPrank (29)) and general alignment/featur”