Welcome to the GitHub repository for Lentivirus-GLUE-SRLV: an extension to Lentivirus-GLUE.
Small ruminant lentiviruses (SRLVs) infect sheep and goats, causing chronic, lifelong diseases that impact various organ systems.
The SRLV extension to SRLV-GLUE incorporates all published SRLV sequence data linked to associated metadata, including information that is sequence-associated (length, publication date); taxonomic (viral genotype, subtype); and isolate-associated (isolation host species, date and location of sampling, isolation source).
The SRLV extension of Lentivirus-GLUE provides functionality for genotyping SRLV sequences via maximum likelihood. Genotyping can be performed on any sequence of adequate length (typically >300 nucleotides are required for confident assignment). Any genomic region can be genotyped using the approach implemented in SRLV-GLUE.
Classification is based on maximum likelihood clade assignment (MLCA) as implemented in GLUE. Sequences are classified into genotypes and subtypes defined via phylogenetic analysis of full-length reference genome sequences.
For more details on the SRLV extension project please see the Lentivirus-GLUE User Guide.
To install Lentivirus-GLUE-SRLV, follow the instructions provided in the User Guide.
You can choose between:
- Docker-based installation for ease of deployment.
- Native installation for traditional setup.
Lentivirus-GLUE-SRLV can be installed as a prebuilt database for quick setup or constructed from scratch via (a project build process) for more customization.
Lentivirus-GLUE-SRLV is constructed using sequence data obtained from NCBI Nucleotide.
We welcome contributions from the community! If you're interested in contributing to Lentivirus-GLUE-SRLV, please review our Contribution Guidelines.
The project is licensed under the GNU Affero General Public License v. 3.0
For questions, issues, or feedback, please open an issue on the GitHub repository.