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GSR: Simulator - EvolveAGene
| Attribute | Value |
|---|---|
| Title | EvolveAGene |
| Short Description | A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions |
| Long Description | EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions, and deletions. |
| Version | 3.06 |
| Project Started | 2008 |
| Last Release | 13 years, 11 months ago |
| Homepage | https://sourceforge.net/projects/evolveagene/?source=navbar |
| Citations | Hall BG, Simulating DNA coding sequence evolution with EvolveAGene 3., Mol Biol Evol, 04-01-2008 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 07-24-2019 (1725 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, Protein Sequence, |
| Variations | Single Nucleotide Variation, Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, Phylip, NEXUS, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | Codon-based, |
| Models | Directional Selection, |
| Recombination | |
| Mutation Models | Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows (Tested only on windows xp), Mac OS X, Linux and Unix (Tested only on ubuntu), |
| Language | Perl, |
| License | |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used EvolveAGene.
2022
Tumescheit C, Firth AE, Brown K, CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments., PeerJ, 03-15-2022 [Abstract]
2019
Thomas AK, Preetha S, Omanakuttan A, Vidyullata L, Ashokan A, Rajachandran V, Chattopadhyay S, Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp., Sci Rep, 03-01-2019 [Abstract]
Yoshimura D, Kajitani R, Gotoh Y, Katahira K, Okuno M, Ogura Y, Hayashi T, Itoh T, Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP., Microb Genom, 05-01-2019 [Abstract]
2018
Cole TJ, Brewer MS, FUSTr: a tool to find gene families under selection in transcriptomes., PeerJ, 01-17-2018 [Abstract]
Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV, Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori., BMC Genomics, 11-21-2018 [Abstract]