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GSR: Simulator - AliSim
| Attribute | Value |
|---|---|
| Title | AliSim |
| Short Description | A fast and versatile phylogenetic sequence simulator |
| Long Description | AliSim is a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly used rate matrix and probability matrix approaches. AliSim takes 1.4 hours and 1.3 GB RAM to simulate alignments with one million sequences or sits, whereas popular software like Seq-Gen, Dawg, and INDELible require 2-5 hours and 50-500 GB of RAM for the same task. |
| Keywords | sequence simulation, phylogenetics, molecular evolution |
| Version | an extension of the IQ-TREE software version 2.2 |
| Project Started | 2011 |
| Last Release | 2 years, 2 months ago |
| Homepage | http://www.iqtree.org/doc/AliSim |
| Citations | Nhan Ly=Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh, AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era, Molecular Biology and Evolution, May 3, 2022 [ Abstract ] |
| GSR Certification |  ✔ Accessibility |
| 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 | Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA, Protein Sequence, Sequencing Reads, Proteomics, |
| Variations | Biallelic Marker, Single Nucleotide Variation, Amino acid variation, Insertion and Deletion, |
| Simulation Method | Machine Learning, Phylogenetic, |
| Input | |
| Data Type | Empirical, Ancestral Sequence, Saved simulation, Other, |
| File format | NEXUS, Phylip, Tree Sequence, Other, |
| Output | |
| Data Type | Phylogenetic Tree, |
| Sequencing Reads | |
| File Format | Phylip, Tree Sequence, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | Multiple Genetic Markers, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | Discrete Models, Continuous Models, |
| Life Cycle | Discrete Generation Model, |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Markov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, |
| Events Allowed | |
| Other | Phenogenetic, Polygenic background, |
| Interface | Command-line, Web-based, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | C or C++, |
| License | Creative Commons, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using AliSim has been provided.
Please propose new citations if you are aware of publications that use this software.