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…
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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…
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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,…
Continue readingPollen/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…
Continue readingLaboratory 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…
Continue readingITS2 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/)….
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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…
Continue readingPollen/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…
Continue reading16S2Genome: 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…
Continue readingHMM 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…
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