The goal of the ENCODE project is to generate a comprehensive catalog of all functional elements. To facilitate this task, members of the consortium have developed and refined software tools.

On this page are brief descriptions of some of the software used to create the ENCODE resource. Software for identifying functional elements, for integrated analysis of multiple data types, and for measuring the quality of the data are described.

On this page are brief descriptions of software and resources that others might find useful for analyzing and using ENCODE data in their own research. Two pieces of software from ENCODE researchers for annotating non-coding regions of the genome (such as SNPs) with features from ENCODE and other resources are presented, as well as a recent chapter in Current Protocols in Human Genetics explaining how to manually inspect genomic regions of interest for ENCODE annotations.

On this page are brief descriptions of some of the software used to create the ENCODE resource. This software was not funded by ENCODE, or devloped by the consortium.