PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. 

Platon detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. It analyses the distribution bias of protein-coding gene families among chromosomes and plasmids.

PoseView automatically creates two-dimensional diagrams of complexes with known 3D structure according to chemical drawing conventions.

Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.

 ProteinsPlus support life scientists in working with protein structures, and focuses on protein-ligand interactions. The server provides support for the initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. 

Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. 

REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites are available for download after the analysis is finished.

Redundans is a pipeline that assists the assembly of heterozygous genomes. It takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. 

ReferenceSeeker determines closely-related reference genomes following a scalable hierarchical approach. It combines a fast kmer profile-based database lookup of candidate reference genomes and subsequent computation of specific average nucleotide identity (ANI) values.

Tools to analyse cis-regulatory elements in genome sequences