Orthologue Finding

orthofinder identification of orthologues

1 Analysis

Orthologue finding was carried out on the protein sequences predicted by prodigal in the directory /assets/analysis/2021-06-22_CDS/proteins using orthofinder v2.5.2. This was run on a CLIMB-MRC server with the command:

orthofinder -t 8 -a 8 -f 2021-06-22_CDS/proteins/ -o 2021-07-07_orthofinder

NOTE: this analysis was not conducted on the Nanopore-only assembly annotations, as their CDS were suspected to be of low quality.

2 Output

Output is placed in the subdirectory /assets/analysis/2021-07-07_OrthoFinder under the following directories:

  • Single_Copy_Orthologue_Sequences: contains 974 multiple sequence (protein) FASTA files containing predicted single-copy orthologues from the 70-genome set of annotated proteins
  • Species_Tree: the species tree built by orthofinder and used for identification of orthologues.
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