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Upcoming Features for LAMARC

Here are some features we plan to add to LAMARC, both in the next release, and in the more distant future.

• Natural selection. We will estimate selection parameters by treating the selected and non-selected alleles as defining "populations" with "migration" due to mutation and recombination allowing haplotypes or sections of haplotypes to move between the "populations".


• Ascertainment bias. We will deal with ascertainment bias (for example, the preferential choice of diseased individuals in case/control studies) by modeling diseased and healthy as "populations".


• Recombination hotspot estimation. We will estimate the presence of recombination hot or cold regions. (Chul Joo Kang is currently working on implementing this in Recombine.)


• Alternative models for growth. Our current model of continuously exponential growth is inadequate for certain populations, and we plan to add both linear and stair-step models of growth (and shrinkage).


• Sequential sampling. Sometimes it is possible to collect or obtain data from multiple generations of your organism (HIV is a good candidate for this). If the mutation rate is known, it is theoretically possible to include this data in a LAMARC-type analysis, and we plan to allow this.

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