realistic simulation of gene family evolution Long Description (required)
PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—perhaps more interestingly—also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. https://code.google.com/p/jprime/
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 23803001 ],
Sjöstrand J, Arvestad L, Lagergren J, Sennblad B ,
GenPhyloData: realistic simulation of gene family evolution. ,
BMC Bioinformatics ,
06-27-2013 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=23803001, Primary Citation
[Pubmed ID: 35106544 ],
Jarvis DE, Maughan PJ, DeTemple J, Mosquera V, Li Z, Barker MS, Johnson LA, Whipple CJ ,
Chromosome-Scale Genome Assembly of Gilia yorkii Enables Genetic Mapping of Floral Traits in an Interspecies Cross. ,
Genome Biol Evol ,
03-02-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35106544, , Application
[Pubmed ID: 35909764 ],
Pelosi JA, Kim EH, Barbazuk WB, Sessa EB ,
Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. ,
Front Plant Sci ,
07-14-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35909764, , Application