Metameric segmentation of the vertebrate body is established during somitogenesis, when a cyclic spatial pattern of gene expression is created within the mesoderm of the developing embryo. The process involves transcriptional regulation of genes associated with the Wnt, Notch, and Fgf signaling pathways, each gene is expressed at a specific time during the somite cycle. Comparative genomics, including analysis of expression timelines may reveal the underlying regulatory modules and their causal relations, explaining the nature and origin of the segmentation mechanism. Using a deconvolution approach, we computationally reconstruct and compare the precise timelines of expression during somitogenesis in chicken and zebrafish. The result constitutes a resource that may be used for inferring possible causal relations between genes and subsequent pathways. While the sets of regulated genes and expression profiles vary between different species, notable similarities exist between the temporal organization of the pathways involved in the somite clock in chick and mouse, with certain aspects (as the phase of expression of Notch genes) conserved also in the zebrafish. The regulated genes have sequence motifs that are conserved in mouse and chicken but not zebrafish. Promoter sequence analysis suggests involvement of several transcription factors that may bind these regulatory elements, including E2F, EGR and PLAG, as well as a possible role of G-quadruplex DNA structure in regulation of the cyclic genes. Our research lays the groundwork for further studies that will probe the evolution of the regulatory mechanism of segmentation across all vertebrates.