AFToL and WASABI
WASABI – Web Accessible Sequence Analysis for Biological Inference:
The AFToL database interface.
F. Kauff, C. J. Cox, and F. Lutzoni
'Fungal trees grow faster with computer help' - Science, Vol 309, Issue 5733, 374 , 15 July 2005.
(click here for PDF format)
Kauff F, Cox CJ, Lutzoni F. 2007. WASABI: An automated sequence processing system for multigene phylogenies. Systematic Biology 56(3):523-531. (click here for PDF)
The goal of the NSF-funded AFTOL (Assembling the Fungal Tree Of Life) project is to enhance the understanding of the evolution of the Kingdom Fungi by sampling 1500+ species for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters. Fungi play pivotal ecological roles: as saprotrophs, they are important in the cycling of nutrients; as pathogens and parasites, they attack virtually all groups of organisms, including bacteria, plants, other fungi, and animals; as mutualistic symbionts, fungi have enabled a diversity of other organisms to exploit novel habitats and resources. Fungi have been found in every ecosystem where they have been sought, including deserts, glacial ice, and deepsea thermal vent communities. For these reasons, a robust fungal phylogeny will greatly enhance our understanding of the history of life.
AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci [nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6 ]. A further objective of this study is to summarize and integrate our current knowledge regarding fungal subcellular features within this new phylogenetic framework.
The name of the bioinformatic package we developed for AFTOL is WASABI (Web Accessible Sequence Analysis for Biological Inference).
WASABI provides an efficient communication
platform to facilitate the collection and dissemination of molecular
data to (and from) the laboratories and participants. All molecular
data can be viewed, downloaded, verified, and corrected by the
participants of AFTOL. A central goal of the WASABI interface is to establish
an automated analysis framework that includes basecalling of
newly generated chromatograms, contig assembly, quality
verification of sequences (including a local BLAST), sequence
alignment, and congruence test. Gene sequences that pass all tests
and are finally verified by their authors will undergo automated
phylogenetic analysis on a regular schedule. Although all steps are
initially carried out noninteractively, the users can verify and
correct the results at any step and thus initiate the reanalysis of dependent data.
All custom made software applications are written in Python (www.python.org) and regularly use modules
provided by BioPython (www.biopython.org).
Click on the colored arrows
for more information.
General information about AFTOL can be obtained at:
For more information about the bioinformatic package developed for AFTOL and to access WASABI go to:
Data section of the AFTOL website
Data sets used in publications of AFTOL can be downloaded at:
AFTOL data sets