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1.  SitePainter: a tool for exploring biogeographical patterns 
Bioinformatics  2011;28(3):436-438.
As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies.
Availability: https://sourceforge.net/projects/sitepainter
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: antoniog@colorado.edu, Rob.Knight@colorado.edu
doi:10.1093/bioinformatics/btr685
PMCID: PMC3268248  PMID: 22171330
2.  TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata 
Bioinformatics  2011;27(21):3067-3069.
Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies.
Results: TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip metadata (e.g. taxonomic labels).
Availability: http://topiaryexplorer.sourceforge.net
Contact: rob.knight@colorado.edu
doi:10.1093/bioinformatics/btr517
PMCID: PMC3198578  PMID: 21903626
3.  UCHIME improves sensitivity and speed of chimera detection 
Bioinformatics  2011;27(16):2194-2200.
Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
Contact: robert@drive5.com
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr381
PMCID: PMC3150044  PMID: 21700674
4.  Boulder ALignment Editor (ALE): a web-based RNA alignment tool 
Bioinformatics  2011;27(12):1706-1707.
Summary: The explosion of interest in non-coding RNAs, together with improvements in RNA X-ray crystallography, has led to a rapid increase in RNA structures at atomic resolution from 847 in 2005 to 1900 in 2010. The success of whole-genome sequencing has led to an explosive growth of unaligned homologous sequences. Consequently, there is a compelling and urgent need for user-friendly tools for producing structure-informed RNA alignments. Most alignment software considers the primary sequence alone; some specialized alignment software can also include Watson–Crick base pairs, but none adequately addresses the needs introduced by the rapid influx of both sequence and structural data. Therefore, we have developed the Boulder ALignment Editor (ALE), which is a web-based RNA alignment editor, designed for editing and assessing alignments using structural information. Some features of BoulderALE include the annotation and evaluation of an alignment based on isostericity of Watson–Crick and non-Watson–Crick base pairs, along with the collapsing (horizontally and vertically) of the alignment, while maintaining the ability to edit the alignment.
Availability: http://www.microbio.me/boulderale.
Contact: jesse.stombaugh@colorado.edu
doi:10.1093/bioinformatics/btr258
PMCID: PMC3106197  PMID: 21546392
5.  PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers 
Bioinformatics  2011;27(8):1159-1161.
Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task.
Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.
Availability: PrimerProspector is open-source software available at http://pprospector.sourceforge.net
Contact: rob.knight@colorado.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btr087
PMCID: PMC3072552  PMID: 21349862
6.  CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes 
Bioinformatics  2009;25(10):1331-1332.
DNA composition in general, and codon usage in particular, is crucial for understanding gene function and evolution. CodonExplorer, available online at http://bmf.colorado.edu/codonexplorer/, is an online tool and interactive database that contains millions of genes, allowing rapid exploration of the factors governing gene and genome compositional evolution and exploiting GC content and codon usage frequency to identify genes with composition suggesting high levels of expression or horizontal transfer.
Contact: rob@spot.colorado.edu
doi:10.1093/bioinformatics/btp141
PMCID: PMC2677738  PMID: 19279067
7.  PyNAST: a flexible tool for aligning sequences to a template alignment 
Bioinformatics  2009;26(2):266-267.
Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).
Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.
Availability: PyNAST is available at http://pynast.sourceforge.net.
Contact: rob.knight@colorado.edu
doi:10.1093/bioinformatics/btp636
PMCID: PMC2804299  PMID: 19914921

Results 1-7 (7)