Software

To make research processes more effective, transparent and reproducible, software tools have been developed by several FLI research groups, with a focus on genome analysis, and structural biology.

Genome Analysis

Bucketer & Sad

Bucketer extracts reads from 2nd generation sequencing data with respect to tag-primer pairs. Sad is used to search in these data. Bucketer and Sad are free for academic and non-profit use.

For commercial usage request a commercial license at koordinator@leibniz-fli.de

Dinucleotide Properties Genome Browser – DiProGB

Genome browser that encodes nucleotide sequences by dinucleotide properties. It is closely linked to DiProDB.

FRAMA 

From RNA-seq data to Annotated MRNA Assembly: Transcriptome assembly and mRNA annotation pipeline for eukaryotes; published in BMC Genomics (2016)

FRAMA utilizes external and newly developed software components to accomplish common post-assembly tasks. These tasks include gene symbol assignment, scaffolding of transcripts, fusion detection and CDS as well as mRNA boundary identification. It is free for academic and non-profit.

For commercial usage request a commercial license at koordinator@leibniz-fli.de

GenALA

Toolkit facilitating prokaryotic genome projects by linking GAP4 assembly and GenColors annotation. It is free for academic and non-profit use. It is free for academic and non-profit use (download at ftp://genome.leibniz-fli.de/pub/software/).

For commercial usage request a commercial license at koordinator@leibniz-fli.de

KILAPE

K-masking and Iterative Local Assembly of Paired Ends: Automated scaffolding and gap filling of de novo genome assemblies. KILAPE is fast, highly scalable, and can be implemented for large and complex genomes on modest hardware. It is free for academic and non-profit use.

For commercial usage request a commercial license at koordinator@leibniz-fli.de

kPerl

A Perl utility package for sequence analysis.

MethTools

Toolbox to visualize and analyze DNA methylation data; published in Nucleic Acids Res (2000).

PosiGene

Program to scan for positively selected genes on a genome-wide scale based on interspecies sequence comparison and codon based methods; supplementary data (download at http://genome.leibniz-fli.de/software/PosiGene/)

RepARK 

Repetitive motif detection by Assembly of Repetitive K-mers: Wrapper script for constructing a repeat library from whole-genome shotgun 2nd generation reads using Jellyfish and either Velvet or CLC; published in Nucleic Acids Res (2014).

It is free for academic and non-profit use. For commercial usage request a commercial license at koordinator@leibniz-fli.de

roche454ace2caf and consed2gap

Tools to convert assemblies from foreign packages (consed with ACE files) to CAF suitable for the Staden package.

Included as "assembly conversion tool" in Bio-Linux distribution.

tuple_plot

A dot plot tool for genome comparison with stochastical background suppression; published in Bioinformatics (2006).

Structural Biology

PREdator

User-friendly Python3-based GUI-driven tool for analysis, evaluation and fitting of series of data points. Stand-alone script for Linux, MacOS and Windows platforms.