BOL

github.com - An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is...

http://www.ub.edu/dnasp/ - DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some...

github.com - ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also...

sourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...

emboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...

http://ggdc.dsmz.de/ - The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C...

tritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...

github.com - GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general,...

csb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...

www.broadinstitute.org - VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in...