MOTIVATION: Conserved non-coding elements (CNEs) represent an enigmatic class of 
genomic elements which, despite being extremely conserved across evolution, do 
not encode for proteins. Their functions are still largely unknown. Thus, there 
exists a need to systematically investigate their roles in genomes. Towards this 
direction, identifying sets of CNEs in a wide range of organisms is an important 
first step. Currently, there are no tools published in the literature for 
systematically identifying CNEs in genomes.
RESULTS: We fill this gap by presenting CNEFinder; a tool for identifying CNEs 
between two given DNA sequences with user-defined criteria. The results 
presented here show the tool's ability of identifying CNEs accurately and 
efficiently. CNEFinder is based on a k-mer technique for computing maximal exact 
matches. The tool thus does not require or compute whole-genome alignments or 
indexes, such as the suffix array or the Burrows Wheeler Transform (BWT), which 
makes it flexible to use on a wide scale.
AVAILABILITY AND IMPLEMENTATION: Free software under the terms of the GNU GPL 
(https://github.com/lorrainea/CNEFinder).