Tools

  • FENNEC: Functional Exploration of Natural Networks and Ecological Communities Assessment of species composition in ecological communities and networks is an important aspect of biodiversity research. Yet, for many ecological questions the ecological properties (traits) of organisms in a community are more informative than their scientific names. Furthermore, other properties like threat status, invasiveness, or human usage are relevant for many studies, but they can ...
  • meta-barcoding marker demultiplexing A single script! What it does: demultiplexing of metabarcoding data which consists of multiple markers. Data must have followed a library preparation/sequencing strategy which includes sequencing of the forward primers. Data must be demultiplexed for samples already. Sequence data must be in forward orientation. The categorization is based on Hidden Markov Model (HHMs) hits of the forward primer within the ...
  • AliTV – Alignment Toolbox and Visualization The comparison of genome structures of organisms can yield interesting insights into evolutionary processes. In order to do the comparison, whole genome alignments are required. However, the interpretation of whole genome alignments is difficult without proper visualization. AliTV utilizes d3.js to create interactive visualizations of whole genome alignments. Example visualizations including the alignment of seven chloroplast ...
  • allocation2samplesheet for Illumina MiSeq A helper script to transform a sample allocation sheet into a samplesheet that can be imported into the Illumina MiSeq for multiplexed sequencing. This repo contains a single script which is mainly for internal usage. Therefore it is not very well documented. But if you want to reuse it, feel free to do it. GitHub: https://github.com/molbiodiv/illumina-allocation-to-samplesheet
  • TBro: visualization and management of de novo transcriptomes A web based transcriptome browser suitable for de novo transcriptomics. It has been used to analyze the Venus Flytrap transcriptome. TBro is a web application that allows biologists to browse the vast amount of data generated by RNA-seq experiments. Powerful search options exist to find transcripts of interest. All information for each transcript is aggregated on ...
  • biojs-io-biom: A JavaScript library for handling data in Biological Observation Matrix (BIOM) format. This library provides an easy to use interface to interact with data in BIOM format. The library itself is written using ES6 and is tested with Mocha. In order to provide compatibility with both versions 1.0 and 2.1 of the BIOM format a lightweight conversion server has been developed. You can find a public instance ...
  • bcgTree: automatized phylogenetic tree building from bacterial core genomes The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due ...
  • Pollen/Plant ITS2 reference set for the RDP/UTAX classifier (2015) Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing. We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that ...
  • Laboratory rearing of solitary bees and wasps Ecological experiments often require standardized methods that exclude natural variation and allow manipulation of a single parameter. It has been shown that domesticated honey bee larvae are raisable in a controlled environment. Here we demonstrate that this approach is also transferable to wild solitary bees and wasps without inducing negative effects on their development. Wells ...
  • ITS2 database update V (with Dept. of Bioinformatics) The internal transcribed spacer 2 (ITS2) is a well-established marker for phylogenetic analyses in eukaryotes. A reliable resource for reference sequences and their secondary structures is the ITS2 database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). However, the database was last updated in 2011. Here, we present a major update of the underlying data almost doubling the number of entities. This ...
  • chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data The chloroExtractor is a perl based program which provides a pipeline for DNA extraction of chloroplast DNA from whole genome plant data. Too huge amounts of chloroplast DNA can cast problems for the assembly of whole genome data. One solution for this problem can be a core extraction before sequencing, but this can be expensive. ...
  • Pollen/Plant ITS2 reference set for the RDP classifier (2014) The identification of pollen plays an important role in ecology, palaeo-climatology, honey quality control and other areas. Currently, expert knowledge and reference collections are essential to identify pollen origin through light microscopy. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach, but the assessment of mixed pollen samples originating ...
  • 16S2Genome: Genomic traits for 16S rDNA microbiota studies Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, whilst genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and ...
  • HMM based ITS2 annotation The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels, whereas its secondary structure is well conserved, and tree reconstructions are possible at higher taxonomic levels. However, annotation ...
  • ITS2 database update III (with Dept. of Bioinformatics) The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, structure ...