title: T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.
abstract: 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.
  
  
  
  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.
  
  
  
  T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.
  
  
  
  icarbon@ncsu.edu.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA.
authors.forename: Ignazio
authors.initials: I
authors.lastname: Carbone
authors.affiliation: Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA.
authors.forename: James B
authors.initials: JB
authors.lastname: White
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jolanta
authors.initials: J
authors.lastname: Miadlikowska
authors.affiliation: School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA.|Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Miller
authors.affiliation: Department of Medicine, University of Giessen, Giessen, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Kauff
authors.affiliation: School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Jana M
authors.initials: JM
authors.lastname: U'Ren
authors.affiliation: Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA.
authors.forename: Georgiana
authors.initials: G
authors.lastname: May
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D060026:Endophytes / Q000502:physiology; D056426:Genetic Loci; D000071253:Metadata; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012984:Software