GSR: Simulator - ALF

Basic Package Attributes
AttributeValue
Title ALF
Short Description A Simulation Framework for Genome Evolution
Long Description Artificial Life Framework (ALF) aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation. ALF is available as a stand-alone application and a user-friendly yet powerful web interface.
Version 0.93
Project Started 2012
Last Release 8 years, 9 months ago
Homepagehttp://alfsim.org/#index
Citations Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C, ALF--a simulation framework for genome evolution., Mol Biol Evol, 04-01-2012 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated11-10-2017 (1072 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence, Protein Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation, Amino acid variation, Insertion and Deletion, Inversion and Rearrangement (Translocation, inversion, inverted translocation), Other (Gc content amelioration, gene duplication/loss, lateral gene transfer, gene fusion/fission),
Simulation MethodPhylogenetic,
Input
Data TypeAncestral Sequence, Other (The user can provide a custom species tree, custom substitution matrices, definitions of regions with different substitution rates),
File formatProgram Specific (Parameter file in darwin format ), Other (Sequences of mrca can be given in fasta format),
Output
Data TypeGenotype or Sequence, Individual Relationship (Orthologs, paralogs, xenologs, gene trees, msas, phylogenetic tree),
Sequencing Reads
File FormatFasta or Fastq, Phylip (Msas), Other (Gene trees and species tree in newick format),
Sample TypeOther (Ancestral sequences at each speciation event are outputted),
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others (Gene duplication/loss, horizontal gene transfer), Heterogeneity among Sites, Others (Gc amelioration, gene fusion and fission, genome rearrangement),
Events AllowedVarying Genetic Features (Change of mutation rates after gene duplication, different substitution and indel models for each branch of the phylogenetic tree, rate vary),
Other
InterfaceCommand-line, Web-based,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageOther (Darwin),
License
GSR CertificationDocumentation,

No example publication using ALF has been provided.

Please propose new citations if you are aware of publications that use this software.


Propose changes to this simulator