Friday, 13 December 2013

LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence

A post on the Evolution Directory (EvolDir) altered me to another classic bioinformatics acronym today: LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence, which has just been updated to version 2.1.9.

“LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its sister program Migrate are successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being supported. The programs are memory-intensive but can run effectively on workstations; we support a variety of operating systems.”

I was all prepared to leap straight in and award LAMARC the coveted pre hoc acronym category for contriving a domain-relevant acronym when I was somewhat halted in my tracks by this statement on the website:

“The LAMARC package is not in any immediate sense derived from the work of Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck(1744-1829). The similarity of names is mostly accidental. But all evolutionary biologists do owe him a debt. Lamarck is an unfairly maligned figure. In addition to being one of the greatest figures of invertebrate biology, he was one of the founders (with Buffon) of the theory of evolution, and the first to propose a mechanism for evolution. You may want to read more about his life and work.”

I am not entirely convinced that the similarity of the names can really be “mostly accidental”, even if that particular acronym did leap out at them once they had the keywords. Either way, the evolutionary link is clear and so, accident or not, I think this warrants a pre hoc rather than post hoc. (Now go and read up on Lamarck.)

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