LineageEvolver - Features
The following is a list of simulation processes implemented in the LineageEvolver 0.9 release.
- Amino Acid Substitution
Using substitution matrix modules, substitutions are processed according to a covarion model. Among Site Rate Variation (ASRV) data is kept on each gene.
- Environmental Variables
Ten environmental variables are kept track of for each organism in the simulation. Each variable mutates automatically and independently as the organism evolves.
- Horizontal Gene Transfer (HGT)
HGT is simulated with weighted randomized selection of candidate organisms using the aforementioned environmental variables to favor selection of organisms that exist in similar environmental conditions. Recombination is processed for each HGT event, recombining portions of a sequence from an origin genome into a destination genome.
- Gene Deletion/Duplication
Genes can duplicate or die off completely in any given genome during the course of evolution. Because orthologs are labeled via the genome naming scheme in the LineageEvolver output, duplicated genes are easily traceable.
As follows is a features list from the developers' point of view. LineageEvolver was built by computer scientists with common programming practices, styles and conventions in mind so as to maintain extensibility and facilitate future development.
- Object Oriented
Constructed from the ground-up in completely object-oriented Java code, LineageEvolver is highly extensible. Abstraction and encapsulation lie at the center of the system structure so as to streamline maintenance and extension procedures.
Because it's based on pure Java, LineageEvolver can run on anything from a traditional personal computer to supercomputers, and everywhere in between. Got a Java-enabled mobile phone? LineageEvolver can technically run on that, too!