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

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

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

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

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.