LineageSpecificSeqgen: A Tool for Simulating Sequence Data with Lineage-Specific Variation
Author Information
Author(s): Liat Shavit Grievink, David Penny, Mike D. Hendy, Barbara R. Holland
Primary Institution: The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University
Hypothesis
How does lineage-specific variation in the proportion of variable sites affect phylogenetic reconstruction?
Conclusion
LineageSpecificSeqgen allows for the simulation of DNA and amino acid sequences that account for lineage-specific evolutionary processes.
Supporting Evidence
- The program allows for the simulation of sequences with changes in the proportion of variable sites.
- It facilitates the development of new methods to identify lineage-specific evolutionary processes.
- The program can be used to test current models of evolution on sequences that have undergone lineage-specific evolution.
Takeaway
This study introduces a program that helps scientists create realistic DNA sequences that change over time, making it easier to study evolution.
Methodology
The program generates datasets based on a rooted tree and specified events, simulating changes in the proportion of variable sites and covarion switch rates.
Digital Object Identifier (DOI)
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