Cactus genome alignments (.hal) for HintermannBoltHawkinsEtAl

This dataset contains genome alignments in .hal format obtained using Progressive Cactus v.2.6.7 (https://doi.org/10.1038/s41586-020-2871-y). The cactus command was used with default parameters to obtain the hal alignments. The alignments represent genomic data for species analyzed in the study "Evolutionary co-option of an ancestral cloacal regulatory landscape during the emergence of digits and genitals" by Hintermann, Bolt, Hawkins et al. 

vertebrate_13way.hal contains whole-genome alignment of follwoing species :

Mus musculusOrnithorhynchus anatinusGallus gallusAnolis carolinensisXenopus tropicalisLatimeria chalumnaeDanio rerioTakifugu rubripesPetromyzon marinusLepisosteus oculatusScyliorhinus caniculaLeucoraja erinaceaAmia calva

mm_zf_lo.hal contains alignments of the HoxD clusters of following species:

Mus musculusDanio rerioLepisosteus oculatus

vertebrate_alignments_genomes.txt lists genome version for each species