Overview
HGTStart v5 predicts horizontal gene transfer (HGT) events for one protein sequence at a time (single-sequence mode). The pipeline reconstructs a phylogenetic tree for your query protein together with its homologs from the built-in database, then infers HGT using the nested-donor logic (AI, hU and hBL indexes), and finally annotates and reports the result in an interactive HTML report.
Pipeline steps: 0 prepare (annotation & grouping) → 1 sub-databases (HOG/Pfam search) → 2 trees → 3 HGT inference → 4 comparison/annotation → 5 report.
Input files
| File | Format | Description |
|---|---|---|
| Protein file | FASTA | Exactly one protein sequence per job. Content after the first space in the header is ignored. |
| Annotation file | GFF / GFF3 / GTF | Annotation of your genome; protein IDs must match the FASTA header. Used for flanking-gene context (steps 3-4). |
| Genome file | FASTA | Genome sequence of the query species (required for HGT inference and context filtering). |
| NCBI taxonomy id | integer | Taxonomy ID of the query species (e.g. 326968 for Ziziphus jujuba). |
Optional parameters
| Parameter | Default | Description |
|---|---|---|
| -sst | diamond | Homolog search engine (DIAMOND, fixed on the web server). |
| -tbt | FastTree | Tree builder: FastTree (fast) or IQ-TREE (accurate). |
| -cut | 70 | Node-support cutoff, 0-100 (e.g. 70 = 70%). 0 skips the candidate cutoff. |
| -don | default groups | Comma-separated donor groups. |
| -opt | self | Optional taxa allowed in the monophyletic ingroup. |
| -ign | none | Taxa to ignore while screening trees. |
| -ssn | 2 | Minimal strongly supported nodes uniting query and donors. |
| -asn | 2 | Minimal number of all supporting nodes uniting query and donors. |
| -mrn | 2 | Minimal number of receptors in a nested position. |
| -mdn | 2 | Minimal number of donors in a nested position. |
| -ogs | 3 | Minimal outgroup size for a tree to be considered valid. |
| -minAI | 0.0001 | Lower bound of the Alien Index for filtering HGT events. |
| -minHU | 0.0001 | Lower bound of the BLAST Score Index (hU) for filtering HGT events. |
| -minHBL | 0.0001 | Lower bound of the Branch Length Index (hBL) for filtering HGT events. |
| -txr | 3 | Taxon resolution for the exogenous test: 1 = phylum, 2 = kingdom, 3 = superkingdom. |
| -flank-n | 1 | Coding loci displayed per side of an HGT block. |
| -timeHGT | off | Enable treePL molecular dating (slower; unresolved dates reported as NA). |
Output
When the job finishes you will receive an interactive HTML report containing the HGT summary table, the phylogenetic tree, the flanking-gene diagram and functional annotations (OG1157 / EGGNOG / PANTHER / SuperFamily / InterProScan / GO / KEGG / Pfam / KO), plus a downloadable archive of all result files. If HGT events are found, each event lists the DonorNode, DNtime, ReceptorNode, RNtime, MSMH_OUT, MSMH_IN, AI, hU and hBL.
Example
On the Predict page you can load a ready-made example with one click: the histone-like HGT gene XP_015873120.1 of Ziziphus jujuba (taxid 326968), which yields a positive HGT result (donor: Bacteria).