From Bioinformatics.Org Wiki
- Artemis - a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
- Ensembl - software system which produces and maintains automatic annotation on eukaryoticgenomes
- ERGO - Automatically annotates and analyzes genomes, identifying the genes and RNAs, assigning functions to the identified proteins and RNAs, and linking the functions to the network of pathways in the organism.
- gff2ps - Converting genomic annotations in GFF format to PostScript
- On-line Genome Annotations - Annotations for many eukaryotic, bacterial and archaeal genomes. Can be searched using accession numbers or sought features
- UGENE - a free and open source DNA and protein sequence viewer and annotation tool.