Example
Exploring gene function by GFICLEE with remove or revise HGT events.
Download test data
- The test data contains:
| File Name | genes/species | Description |
|---|---|---|
| input_gene_set.txt | 17 | The gene set from human pathway Nucleotide excision repair |
| human_profile.txt | 2620 | This phylogenetic profile includes 2620 genes. |
| species_tree_138.nwk | 138 | The Species tree includes 138 Organisms. |
| 138_Taxa.txt | 138 | The Taxonomy file of 138 species. |
Download test data : TestData2
Uncompress
tar -zxvf TestData2.tar.gz
cd TestData
Run GFICLEE with "-rm" option.
$ java -jar GFICLEE1.0.jar -i input_gene_set.txt -p human_profile.txt -t species_tree_138.nwk -rm 138_Taxa.txt -o output_file.txt
GFICLEE: Started with arguments: -i input_gene_set.txt -p human_profile.txt -t species_tree_138.nwk -rm 138_Taxa.txt -o output_file.txt
Read Taxonomy file completed...
Found 37 animals
Found 16 plants
Found 56 fungi
Found 29 protists
Detecting the suspicious HGT event...
Detecting suspicious HGT by animals subgroup: 810 genes
Detecting suspicious HGT by plants subgroup: 936 genes
Detecting suspicious HGT by fungi subgroup: 1142 genes
Detecting suspicious HGT by protists subgroup: 1413 genes
Total infer suspicious HGT: 3732 genes
Warning: removing 3732 genes from the phylogenetic profile.
GFICLEE: Completed successfully
Time used: 5.59 Seconds
Run GFICLEE with "-rv" option.
$ java -jar GFICLEE1.0.jar -i input_gene_set.txt -p human_profile.txt -t species_tree_138.nwk -rv 138_Taxa.txt -o output_file.txt
GFICLEE: Started with arguments: -i input_gene_set.txt -p human_profile.txt -t species_tree_138.nwk -rv 138_Taxa.txt -o output_file.txt
Read Taxonomy file completed...
Found 37 animals
Found 16 plants
Found 56 fungi
Found 29 protists
Detecting the suspicious HGT event...
Detecting suspicious HGT by animals subgroup: 810 genes
Detecting suspicious HGT by plants subgroup: 936 genes
Detecting suspicious HGT by fungi subgroup: 1142 genes
Detecting suspicious HGT by protists subgroup: 1413 genes
Total infer suspicious HGT: 3732 genes
Warning: revising 3732 genes in the phylogenetic profile.
GFICLEE: Completed successfully
Time used: 6.941 Seconds
Notice: using the filter HGT option, users should prepare the Taxonomy's file (split by Tab) consistent with the species tree. For example, The "138_Taxa.txt " file that queries the taxonomy from KEGG organism list.