Data for study on Baltic herring evolution

This repository contains datasets used to characterize molecular evolution and adaptive variation in the Atlantic herring (Clupea harengus) from the Baltic Sea. Contents o gene_models.tar.gz species.tsv: a list of nine clupeiform species used in the study, including the abbreviation/tag used to label their sequences. <tag>.cds.fasta, <tag>.protein.fasta, <tag>.list.tsv: a set of protein coding genes for each species, including the coding sequences as nucleotides (cds; FASTA) or amino acids (protein; FASTA) and a table that either translates between internal tagged and numbered sequences names and their corresponding canonical labels in NCBI or ENSEMBL (in case of previously published data) or shows the template sequence used to detect the gene (in case of novel gene models) (TSV format). Contents of LRRC8C.tar.gz Data for LRRC8C1/2 genes: LRRC8C.accessions.tsv: accessions of sequences downloaded from Ensembl or NCBI (TSV format) LRRC8C.AA.fasta: amino acid alignment (FASTA format) LRRC8C.CDS.fasta: the corresponding nucleotide alignment (FASTA format) LRRC8C.CDS.nexus: the corresponding nucleotide alignment (NEXUS format with MrBayes block) LRRC8C.CDS.mrbayes.con.tre: the majority-rule consensus tree with Bayesian Posterior Probabilities (Newick format) codeml.out: the main output text file generated by PAML (simple text) Contents of FTG.tar.gz Data for F13A and FTG genes: AA_aln.fasta: amino acid alignment (FASTA format) CDS_aln.fasta: the corresponding nucleotide alignment (FASTA format) codon_based_ML_tree_BS.treefile: the maximum likelihood tree with bootstrap values (Newick format) codeml.out: the main output text file generated by PAML (simple text) Contents of hatching_enzyme.zip mature_hatching_enzyme_AA_aln.fa: amino acid alignment (FASTA format) mature_hatching_enzyme_CDS_aln.fa: the corresponding nucleotide alignment (FASTA format) mature_hatching_enzyme.treefile: codon model maximum likelihood tree with bootstrap values (Newick format) HE1C_and_flanking_genes_gff3: annotation files for HE1C and flanking genes on Atlantic herring chromosome 26 from haplotype-phased PacBio assemblies (GFF3 format)