Motivation: High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. Results: In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi - Pezizomycotina (Ascomycota) - based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree.
Bibliographical noteFunding Information:
for the development of T-BAS was provided by the National Science Foundation (NSF) Dimensions of Biodiversity (DoB) program to IC (DEB-1046167), AEA (DEB-1045766) and FL (DEB-1046065). Maintenance and future development of T-BAS v1.0 is supported by the National Science Foundation (NSF) Genealogy of Life (GoLife) program to IC (DEB-1541418), AEA (DEB-1541496) and FL and JM (DEB-1541548). The CIPRES RESTful API is supported by NSF DBI-1262628 and a generous award (TG-DEB090011) of computer time and development support from the XSEDE project (also sponsored by the U.S. National Science Foundation).
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