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

Abstract

Background: Phylogeny-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.

Results: We 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 .

Conclusions: The 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.

Figure 1

The webPRANK submission page has a modular, easy-to-use interface and contains integrated documentation explaining the main features. In addition to submission of new tasks and retrieval of finished jobs, the site allows uploading of existing alignments to a web-based alignment browser for visualisation and post-processing.

Figure 2

Resulting alignments, and uploaded alignments in HSAML format, can be displayed and post-processed using a powerful alignment browser. The alignments are shown alongside the guide tree relating the sequences; the tree is interactive and allows control of the information tracks displayed. (A) The site-wise alignment reliability is indicated in shades of grey (bottom). Unreliably aligned sites are deselected (columns marked grey) using an adjustable threshold (drop-down 'Reliability' menu) and the remaining sites can be exported in various alignment formats for downstream evolutionary analyses. (B) Using the FAST/SLOW/CODON model, inferred sequence structure for genomic DNA alignments is indicated in shades of green, red and blue (bottom). A prediction for a pre-computed EPO alignment [16] shows a correctly inferred change from the FAST state (green) in the intron through the SLOW state (red) at the splice site to the three CODON states (blue) in the exon.