What do I do ?

Horizontal gene transfer (HGT) is the transmission of genetic material between species by ways other than direct (vertical) inheritance from parents to the offspring. HGT is recognized as a major evolutionary force in prokaryotes as it is involved, for example in acquisition of antibiotic resistance or pathogeny. HGT has long been overlooked and considered insignificant in eukaryotes. However, HGT have also played important roles in the evolutionary history and biology of these species, including in animals (1). For example, HGT have contributed to the colonization of land by plants, in the emergence of plant parasitism in nematodes or in the development of capabilities like resistance to extreme temperatures or desiccation in various animals. Progress in genome sequencing technologies has allowed multiple plant, fungal and animal genomes to be publicly released. Systematic searches for HGT events in the root-knot nematodes or in the bdeloid rotifer, have shown that between 3 and 9 % of protein-coding genes in these species were probably of non-animal origin (2,3). However, in the absence of a user-friendly, rapid, and publicly available tool to detect HGT events in any taxonomic group of interest, we still lack a global view of the prevalence of HGT across a tree of life. Here, we propose Alienness, a taxonomy-aware web application that parses homology search (BLAST, Diamond) results against public libraries to rapidly identify candidate HGT in a genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any protein library providing taxonomic information on hits. The user defines recipient (e.g. metazoan) and donor (e.g. bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the homology search results, Alienness calculates three scores for rapid detection of HGT events: (i) the Alien Index (AI) metrics as described in (4) to detect a significant gap of magnitude in e-values between candidate donor and recipient taxa. (ii) The HGT Index, based on the same principle but using bit-scores instead of e-values as defined in (5). (iii) The Aggregative Hit Score (AHS) based on a normalized sum of candidate donor and recipient bit scores as defined in (6). Alienness provides a series of useful output and allows taxonomically aware exploration of blast / diamond results. The output generated can also be used for phylogenetic confirmation and exploration via the AvP software (6), available at: https://github.com/GDKO/AvP. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

1. Danchin. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biology (2016). (View Online)
2. Paganini et al. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PLoS One (2012). (View online)
3. Flot et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga, Nature (2013). (View Online)
4. Gladyshev et al. Massive horizontal gene transfer in bdelloid rotifers, Science (2008). (View Online)
5. Boschetti et al. Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers. PLoS Genetics (2012). (View Online)
6. Koutsovoulos et al. AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers. PLoS Computational Biology (2022). (View Online).

What's news ?

Update version 3.0 _ 2024-02-29

New input format
Alienness takes as input the BLAST or DIAMOND result of a proteome performed against a protein database. A standard format with an additional taxid column is now expected. You must set the outfmt option of blast as follows: -outfmt 'X std staxid' with X = 6 (Tabular) or X = 7 (Tabular with comment lines).
AHS score calculation
We developed a new metric called Aggregate Hit Support (AHS). Now available in this version of alienness.
AvP: A Software Package for Automatic Phylogenetic Detection of Candidate Horizontal Gene Transfers.
Koutsovoulos, Georgios D., Solène Granjeon Noriot, Marc Bailly-Bechet, Etienne G. J. Danchin, et Corinne Rancurel. PLOS Computational Biology (2022) (View Online).

AvP : Alienness versus Predictor _ 2020.12.01

Phylogenetic analysis is necessary to more robustly confirm HGT candidates. Also, alienness team present AvP ( Alienness versus Predictor) to automatically detect candidate HGTs within a phylogenetic framework. It is accessible under GNU General PublicLicense v3.0 at https://github.com/GDKO/AvP pending the implementation of the AvP module in the Alienness web server. AI features file is necessary to use AvP. This file is now available in the result archive of the alienness tool.

Update version 2.0 _ 2020.12.01

Using Accession.version Numbers instead of GI Numbers
NCBI is in the process of changing the way we handle GI numbers for sequence records. As part of this transition, we have make appropriate updates. The new version of Alienness henceforth uses output blast or diamond formats where each line contains the accession.version instead of gi.
More input formats accepted
Now, you can provide outformat six or seven for blast tool, or standard output of diamond.
Calculation of the HGT index
In addition to the Alien Index (AI), the HGT index is calculated.
Supporting donors
This version of Alienness evaluates the number of donor hits that supports the detected HGT taxon for each queries.
Visual exploration of blast results
Alienness offers an html index that allows visual exploration of the blast results, in particular by means of color coding. The novelty lies in the comparison of each lineage of hits following the donor to the donor's lineage. These hits are grouped together as long as they share the same node with the donor. Each button contains the lineage shared with the donor.

More information

Date of update

Alienness release
Latest ncbi session
Taxonomy: 2024-03-19

Example of results

Meloidogyne incognita
Taxonomic group of interest
Metazoa 33208
Taxon group(s) to exclude
Tylenchomorpha 33283

Dataset Download

blast output: 32 queries of
Meloidogyne incognita
You can test with :
Taxonomic group of interest
Metazoa 33208
Taxon group(s) to exclude
Tylenchomorpha 33283


Alienness: Rapid detection of horizontal gene transfers in metazoan genomes
(View Online)
Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.
Genes 2017, 8(10), 248;
(View Online)