Table 2.
Representative methods in all citations.
| Name of the method | Uniform resource locator | Description | References |
|---|---|---|---|
| Pangolin | https://github.com/cov-lineages/pangolin | A lineage nomenclature, whose beginning letter represents the pedigree followed by dots and letters to indicate the descendant branches. | [20] |
| PhyCLIP | https://github.com/alvinxhan/PhyCLIP | Phylogenetic clustering by linear integer programming (PhyCLIP), a statistically principled phylogenetic clustering approach and a lineage nomenclature which is used by GISAID. | [21] |
| Nextstrain | https://nextstrain.org/ncov/gisaid/global/6m | The lineage nomenclature created by Nextstrain which is named after the time when a virus variant appeared. | [22] |
| Nextflu | https://nextflu.org | A workflow and visualization program capable of analyzing and exploring the latest influenza virus sequence data. | [32] |
| UShER | https://genome.ucsc.edu/cgi-bin/hgPhyloPlace | A tree-based data framework which encodes the inferred evolutionary history of the virus to improve the speed of phylogenetic analysis. | [35] |
| VENAS | https://github.com/qianjiaqiang/VENAS | The viral genome evolutionary analysis system (VENAS), a software providing integrated analysis of genomic variations which reduces time and computation cost. | [36] |
| VarEPS | https://nmdc.cn/ncovn/ | An evaluation and prewarning system for SARS-CoV-2 which includes known and virtual mutations to achieve rapid evaluation of the risks posed by mutant strains. | [46] |
| PyR0 | https://github.com/broadinstitute/pyro-cov/tree/v0.2.1 | A pipeline based on hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions and identifies mutations relevant to fitness. | [47] |
| SpikePro | https://github.com/3BioCompBio/SpikeProSARS-CoV-2 | A simplified computational model which enables to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. | [60] |
| SAS | https://www.biosino.org/sas | A platform which can predict the resistant effect of emerging variants and the dynamic coverage of SARS-CoV-2 antibodies among circulating strains. | [61] |
| STHAM | https://github.com/uofu-ccts/prisms-comp-model-stham | Spatio-temporal human activity model (STHAM), a kind of extended agent-based model which enables to simulate SARS-CoV-2 transmission dynamics. | [67] |
Abbreviations: GISAID, the Global Initiative on Sharing All Influenza Data; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.