GSR: Simulator - AliSim

Basic Package Attributes
AttributeValue
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
Homepagehttp://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 CertificationGSR-certified

Accessibility
Documentation
Application
Support

Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA, Protein Sequence, Sequencing Reads, Proteomics,
VariationsBiallelic Marker, Single Nucleotide Variation, Amino acid variation, Insertion and Deletion,
Simulation MethodMachine Learning, Phylogenetic,
Input
Data TypeEmpirical, Ancestral Sequence, Saved simulation, Other,
File formatNEXUS, Phylip, Tree Sequence, Other,
Output
Data TypePhylogenetic Tree,
Sequencing Reads
File FormatPhylip, Tree Sequence,
Sample TypeRandom or Independent,
Phenotype
Trait Type
DeterminantsMultiple Genetic Markers,
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
SpatialityDiscrete Models, Continuous Models,
Life CycleDiscrete Generation Model,
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others,
Events Allowed
OtherPhenogenetic, Polygenic background,
InterfaceCommand-line, Web-based,
Development
Tested PlatformsWindows, Linux and Unix,
LanguageC or C++,
LicenseCreative Commons,
GSR CertificationAccessibility, Documentation, Application, Support,

Number of Primary Citations: 1

Number of Non-Primary Citations: 0

No example publication using AliSim has been provided.

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