This directory contains data related to producing whole genome alignments and identifying conserved elements. Due to size, the main whole genome alignment is not included, but it can be accessed as part of the UCSC track hub available here:https://ifx.rc.fas.harvard.edu/pub/ratiteHub8/ Directories: cormorant: code and alignment file (HAL format) for creating a five-way alignment between chicken and cormorant genomes for the purposes of extracting CNEEs from these species. cons_elem_id: data related to running PHAST to identify conserved elements based on the whole genome alignment. scripts: code and related files. See README in scripts subdirectory for more information Primary data files are also located in the cons_elem_id subdirectory: ce_annotation.tsv contains a range of annotation information for each conserved element galGal4 bed files for all CNEEs >50 bp and for all conserved elements are also included