GFICLEE is a program for predicting the new members in biological pathway or biological complex. It is based on the common loss events in gene evolution. When input a gene set in same biological pathway, this program will scan all reference genome predict potential members of this pathway. This program requires three inputs, (1) the gene set in same biological pathway or biological complex, (2)a binary species tree, (3) the binary phylogenetic profile of all genes in this reference genome across the species.
| Option | Description |
|---|---|
| -i | Input gene set in the same pathway or complex. |
| -p | The binary phylogenetic profile. |
| -o | Result file Path. |
| -t | The species tree in Newick format. |
| -c | Predicted with multi threads. The default is 1. |
| -m | Choose predict model<'eq','h','l','lh'>. the default model is 'eq'. |
| -rm | Remove the suspicious HGT events in phylogenetic profile (need provide taxonomy file). |
| -rv | Revise the suspicious HGT events from phylogenetic profile (need provide taxonomy file). |
java -jar GFICLEE1.0.jar -i input_gene_set.txt -p phylogenetic_profile.txt -t species_tree.nwk -o output_file.txt
Detail document : https://yangfangs.github.io/GFICLEE1.0/
Cite: Fang, Y., Li, M., Li, X. et al. GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level. BMC Genomics 22, 774 (2021). https://doi.org/10.1186/s12864-021-08070-7