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GSR: Simulator - ALF
| Attribute | Value |
|---|---|
| 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 | 12 years, 3 months ago |
| Homepage | http://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 |
| Last evaluated | 11-10-2017 (2346 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, Protein Sequence, |
| Variations | Biallelic 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 Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, Other (The user can provide a custom species tree, custom substitution matrices, definitions of regions with different substitution rates), |
| File format | Program Specific (Parameter file in darwin format ), Other (Sequences of mrca can be given in fasta format), |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship (Orthologs, paralogs, xenologs, gene trees, msas, phylogenetic tree), |
| Sequencing Reads | |
| File Format | Fasta or Fastq, Phylip (Msas), Other (Gene trees and species tree in newick format), |
| Sample Type | Other (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 Models | Markov 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 Allowed | Varying Genetic Features (Change of mutation rates after gene duplication, different substitution and indel models for each branch of the phylogenetic tree, rate vary), |
| Other | |
| Interface | Command-line, Web-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | Other (Darwin), |
| License | |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used ALF.
2022
Briand S, Dessimoz C, El-Mabrouk N, Nevers Y, A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem., Syst Biol, 10-12-2022 [Abstract]
Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C, Read2Tree: scalable and accurate phylogenetic trees from raw reads., bioRxiv, 12-13-2022 [Abstract]