Supplementary_files.zip

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 14.0px 'Times New Roman'; color: #00000a; -webkit-text-stroke: #00000a} span.s1 {font-kerning: none} p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Times New Roman'; color: #00000a; -webkit-text-stroke: #00000a; background-color: #ffff00} p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Times New Roman'; color: #00000a; -webkit-text-stroke: #00000a; background-color: #ffff00; min-height: 15.0px} p.p3 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Times New Roman'; color: #00000a; -webkit-text-stroke: #00000a} span.s1 {font-kerning: none} span.s2 {font-kerning: none; background-color: #ffff00} <b>Data_Supp1.</b> Summary of the number of genes retrieved from each species and for each gene set, along with the number of pseudogenes and the number of LoF mutations. <br> <b>Data_Supp2.</b> Sequences predicted with exonerate and ID of sequences retrieved from Ensembl. <br> <b>Data_Supp3.</b> Results obtained with different methods for dating relaxed selection on eye genes in <i>Lucifuga dentata</i>. <br> Description of Supplementary files content: Divergence_values: Pairwise nucleotidic distances between species for each gene set. Lucifuga_Supplementary_files_Genome: Original GFF3 file with functional annotations and scaffolds smaller than 200 bp not uploaded to NCBI. MutPred2_Results: Raw output of MutPred2. Parsed results files to be used with the script provided in github (MutPred2_Script.R) are also provided. Phylogenies: Gene phylogenies computed with iQTree and displayed with iTOL. The model used for each phylogeny can be found on the “Models” folder. Concatenated_Alignments: Concatenated alignments for vision, circadian and pigmentation genes.<br>