Geneious Server™ sequence analysis software package is designed specifically for high-intensity computing such as next-generation sequencing. It builds on the desktop sequence analysis software Geneious Pro. Geneious Server lets users offload large sequence-analysis jobs to servers and computing clusters, harnessing institutions’ existing computational resources from the Geneious Pro interface. The server combines peer-reviewed and open-source assembly and alignment algorithms with visualization tools in one application. Geneious Server runs on a 64-bit Red Hat Linux server and can either run as a server workstation or can submit jobs to computing clusters using the Oracle/Sun Grid Engine.