3. Comparative population transcriptomics in krill: orthogroups (FASTA, TSV files)

This item contains a gzipped archive with ~13,000 orthogroups used to study molecular evolution in this project.

Archive:

krill.orthogroups.tar.gz

Contents of archive (FILE,SIZE,SPECIES,SAMPLES,SNPs):

• krill.proteinortho.tsv - the primary output table from Proteinortho. Describes which protein sequences from which species belong to the same orthogroup. Format according to the standard output of the program.
• krill.proteinortho.tsv.seqs.csv - a processed table that also contains the actual sequences line by line (see below).
• the alignments directory, which contains all OGs in unaligned and aligned files in FASTA format (see below).
  Format of the krill.proteinortho.tsv.seqs.csv table

The fields are:

• NR = orthogroup number
• ORTHO_GROUP = orthogroup ID
• N_SPECIES = the number of species
• N_GENES = the number of genes/sequences in this orthogroup
• N_MATCHING[o] = number of sequences matching outgroup species for this orthogroup
• N_NON_MATCHING = number of sequences matching ingroup species for this orthogroup
• HEADER = the name of this particular sequence
• SEQ = the protein sequence
  Contents of the alignments directory

Each orthogroup is represented by up to four FASTA files:

• OG*.cds.ginsi.fasta.orig = the original, unaligned and unfiltered sequences
• OG*.cds.ginsi.fasta = the aligned and filtered sequences
• OG*.cds.ginsi.fasta.without_cold_euphausia.fasta = the aligned and filtered sequences after removing cold-associated Euphausia species
• OG*.cds.ginsi.fasta.without_cold_thysanoessa.fasta = the aligned and filtered sequences after removing cold-associated Thysanoessa species