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SysBioChalmers / HGTphyloDetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
MIT License
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evolutionary-biology high-throughput-pipeline horizontal-gene-transfer phylogenetics sequence-analysis systems-biology

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HGTphyloDetect

Horizontal gene transfer (HGT) refers to the exchange of genetic material between disparate groups of organisms other than from parent to offspring, which has been confirmed as a very significant factor in adaptive evolution, disease emergence and metabolic shift that can act across various species. However, current methods for HGT detection are usually not automatic, narrow applicable or unavailable to use. In this work, we developed a versatile computational toolbox named HGTphyloDetect by combining a high-throughput pipeline together with phylogenetic analysis to facilitate comprehensive investigation of the potential mechanism for HGT events. Tests on two case studies suggest that this approach could effectively identify horizontally acquired genes with high accuracy. In-depth phylogenetic analysis further facilitates the navigation of the potential donors and detailed gene transmission process. The HGTphyloDetect toolbox is designed for ease of use and could accurately find HGT events with a very low false discovery rate in a high-throughput manner.

HGT identification pipeline

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Citation

Please cite this paper: Yuan, Le, et al. HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer. Briefings in Bioinformatics (2023). https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbad035/7031155.

Installation

Install the latest version with:

$ git clone https://github.com/SysBioChalmers/HGTphyloDetect.git
$ cd HGTphyloDetect
$ pip install -r requirements.txt

Please note: this is sufficient to run the HGT detection functionality of HGTphyloDetect. Additional software dependencies and installation instructions are specified in the User tutorial.

Example

We provide a user-friendly example for small test, users just need to prepare a FASTA file including protein id and protein sequence, note that protein id should be from the GenBank protein database.

(1) If you are now in the HGTphyloDetect directory, just enter into the folder example via the command line:

cd example

(2.1) Then users can run the script for the input file (default AI value = 45, out_pct = 0.90): 

python HGT_workflow.py input.fasta

(2.2) If users want to change the default values for the parameters used in the pipeline, e.g., AI value = 40, out_pct = 0.80, just reset the constant values and run the following: 

python HGT_workflow.py input.fasta AI=40 out_pct=0.80
(3) Finally, our software could generate the output results as a file under the folder example for this gene/protein. The output file includes some important information, i.e., Alien index, E value and donor information. For example: Gene/Protein Alien index E value Donor id Donor taxonomy
AAT92670 199.18 3.15e-87 WP_208929673 Bacteria/Firmicutes

User Manual

Please check the documentation User tutorial for the user manual. Here you can download this file for your case studies.

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