Identification of transcriptionally verified X. index-specific proteins

Using the Orthofinder results generated that regrouped homologous nematode protein sequences into orthogroups, these orthogroups are filtered to identify the ones that contain only X. index sequences. These ones are considered orphan proteins (specific to X. index). Also, some X. index proteins were singletons and not classified in any of the orthogroups. These are also considered orphans. Then, using transciptomics data, a list of X. index genes with verified transciption is obtained by filtering the RNA-seq result file by FPKM. If an orphan orthogroup contained at least 1 expressed gene, all sequences from the orthogroup is considered expressed.