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GSR: Simulator - AliSim-HPC
| Attribute | Value |
|---|---|
| Title | AliSim-HPC |
| Short Description | parallel sequence simulator for phylogenetics |
| Long Description | AliSim-HPC, which, for the first time, employs high-performance computing for phylogenetic simulations. AliSim-HPC parallelizes the simulation process at both multi-core and multi-CPU levels using the OpenMP and message passing interface (MPI) libraries, respectively. AliSim-HPC is highly efficient and scalable, which reduces the runtime to simulate 100 large gap-free alignments (30 000 sequences of one million sites) from over one day to 11 min using 256 CPU cores from a cluster with six computing nodes, a 153-fold speedup. While the OpenMP version can only simulate gap-free alignments, the MPI version supports insertion-deletion models like the sequential AliSim. |
| Version | v.2.3.6 |
| Project Started | 2024 |
| Last Release | 11 months, 2 weeks ago |
| Homepage | https://github.com/iqtree/iqtree2/releases |
| Citations | |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | Tree Sequence, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 0
Number of Non-Primary Citations: 1
The following 1 publications are selected examples of applications that used AliSim-HPC.
2023
Ly-Trong N, Barca GMJ, Minh BQ, AliSim-HPC: parallel sequence simulator for phylogenetics., Bioinformatics, Sept. 2, 2023 [Abstract]