Web Resources & Software

It is part of good scientific practice and further backed by our open access strategy to make research procedures, tools, results, and databases accessible to the scientific communitiy and the public. Here, we provide you with freely accessible web resources and software tools which were developed by FLI research groups.

If you have any questions, just get in contact with our webserve team.

Genome Analysis

• GenColors
  Web-based software/database system aimed at an improved and accelerated annotation and finishing of microbial genomes taking into account information on related genomes and making extensive use of genome comparison analyses. Under this link you will find a number of genome servers having these features but including only genomes for which annotation process is finished.
• Dinucleotide Properties Database – DiProDB
  Database designed to collect and analyze thermodynamic, structural and other dinucleotide properties.
• Nothobranchius furzeri Information Network Genome Browser - NFINgb
  Genome browser providing access to the genome assembly and annotation of the short-lived teleost fish Nothobranchius furzeri.
• Nothobranchius furzeri Information Network Transcriptome Browser - NFINtb
  Database of de novo assembled and annotated cDNA contigs of the short-lived teleost fish Nothobranchius furzeri.
• TAndem Splice Site DataBase - TassDB
  Database offering extensive information on alternative splice events at tandem donors and acceptors, including both confirmed and unconfirmed cases.

Structural Biology

• Jena3D Viewer
  Jmol-based viewer for molecular 3D structures. It is an integral part of JenaLib but can also be used as a standalone version for newly solved structures, for example.

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