This repository contains the code employed to investigate the hagfish genome, as well as key data files.
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Supplementary File 1. Table gathering essential information for each gene model in E. atami including location, protein domains, gene family, gene expression cluster Eptata_genes_filt.xlsx
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Supplementary File 2. Number of orthologues (mutual-best-hits) shared between hagfish and lamprey chromosomes. Pata-Pmar_syntCounts.txt
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Supplementary File 3. Phylogenetic trees inferred for paralogons in each CLG assuming the C20+R model paralogons_t6_c20.pdf
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Supplementary File 4. Synteny-based paralogue classification for reconstructed gene families Vert_Evt_OGrrA.txt.
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Supplementary File 5 Functional enrichment for sets of paralogues showing distinct retention patterns after genome duplications in vertebrates (Fig. 4b) Vert2R_Go_enrich_wg_gds.txt.
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Supplementary File 6. List of gene families labelled with their origin and lineage-specific losses all_families_gain_loss.txt
Detail about analyses conducted in the paper are specified in the different subfolders.
