Getting start
GFICLEE is implemented in Java programming language, Supporting Linux, Windows, and Mac os platforms.
Install
install Java
GFICLEE support Java8 or late
- For Fedora/Cent OS
sudo dnf install java-1.8.0-openjdk
- For Ubuntu/Debian
sudo apt-get install default-jre
Downloading GFICLEE
Usage
GFICLEE is a command line program, should execute in console or shell.
java -jar GFICLEE1.0.jar -i input_gene_set.txt -p phylogenetic_profile.txt -t species_tree.nwk -o output_file.txt
Basic options
| Option | Description |
|---|---|
| -i | Input gene set in the same pathway or complex. |
| -p | The binary phylogenetic profile. |
| -o | The predict result file name. |
| -t | The species tree with nwk 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). |