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GSR: Simulator - DAWG
| Attribute | Value |
|---|---|
| Title | DAWG |
| Short Description | An application designed to simulate the evolution of recombinant DNA sequences in continuous time |
| Long Description | DNA Assembly with Gaps (Dawg) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users. Dawg records the gap history of every lineage to produce the true alignment in the output. Many options are available to allow users to customize their simulations and results. |
| Version | 1.2 |
| Project Started | 2006 |
| Last Release | 15 years ago |
| Homepage | https://github.com/reedacartwright/dawg |
| Citations | Cartwright RA, DNA assembly with gaps (Dawg): simulating sequence evolution., Bioinformatics, 11-01-2005 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 06-27-2019 (1752 days ago) |
| 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 | Haploid DNA Sequence, |
| Variations | Single Nucleotide Variation, Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, Phylip, NEXUS, Other (Clustal), |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, |
| Mutation Models | Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows (Mingw), Mac OS X, Linux and Unix, Solaris, Others (Freebsd, iris), |
| Language | C or C++, Perl, |
| License | |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used DAWG.
2022
van der Putten BCL, Huijsmans NAH, Mende DR, Schultsz C, Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution., Microb Genom, 03-01-2022 [Abstract]
Ly-Trong N, Naser-Khdour S, Lanfear R, Minh BQ, AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era., Mol Biol Evol, 05-03-2022 [Abstract]