Software

List of provided software

Chromatic Dot Plot
NGS tools for the novice
SOA
easyPAC
proTRAC
QuickPick


Chromatic Dot Plot:

Chromatic Dot Plot can be used to identify and display regions of high and low similarity within one sequence (e.g. interspersed repeats or tandem repeats) or between two different sequences. Furthermore, the color coding allows to identify diagonals even in dotplots that are saturated with low quality matches and thus without the need for multiple testing and adjusting of parameters.

 

 

Download Chromatic Dot Plot
Download Chromatic Dot Plot (documentation)

 

NGS tools for the novice

This NGS toolkit provides a set of simple command line based Perl scripts for basic analysis and processing of next generation sequencing datasets. The range of functions comprises sorting by TAGs, clipping of TAGs, FASTQ to FASTA conversion, mapping to reference sequences, eleminating and counting of redundant sequences, Phred score (quality score) based sequence filtering, FASTQ quality analysis etc.
Single scripts can easily be combined to personalized and powerful pipelines via simple batch files.

 

Download NGS tools for the novice (deposited at sourceforge.net)
Instructions

 

SOA:

SOA is a software to evaluate spatial overlap of two groups of individuals based on pairwise spatial distances. It was used in a population genetic study to reveal and quantify differences in the spatial overlap of two mouse lemur species in different habitats (Hapke A, Gligor M, Rakotondranary SJ, Rosenkranz D, Zupke O. Hybridization of mouse lemurs: different patterns under different ecological conditions. BMC Evol Biol. 2011 11:297 doi:10.1186/1471-2148-11-297)

 

Download SOA
Download SOA (documentation)

 

easyPAC:

easyPAC is a comfortable tool for fast prediction of degenerate primers from alignments and consensus sequences. It applies all standard quality tests to degenerate primers and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity. You will find detailed information in the easyPAC paper: Rosenkranz D. easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences. Evolutionary Bioinformatics 2012 8:151-159.

Download easyPAC
Download easyPAC (documentation)
Download easyPAC viedeo abstract (deposited at sourceforge.net)   mp4  avi  wmv

 

proTRAC:

Probabilistic detection, visualization and analysis of piRNA clusters using NGS sequence data. proTRAC shows higher sensitivity and selectivity compared to hitherto applied methods of cluster detection. Citation: Rosenkranz D and Zischler H. proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics 2012 13:5 doi:10.1186/1471-2105-13-5

 

Download proTRAC
Download proTRAC (documentation)
QuickStart and Troubleshooting


QuickPick:

QuickPick is a handy tool to pick inserts from vector sequences. QuickPick will find inserts irrespective of ligation direction by searching primer sequences in sense and antisense orientation allowing up to five mismatches including insertions and deletions.

 













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