Oblong, a program to analyze phylogenomic data sets with millions of characters, requiring negligible amounts of RAM

GOLOBOFF, PABLO A.

Rostock

Congreso; XXXII International Meeting of the Willi Hennig Society; 2013

Willi Hennig Society

Oblong, a program with very low memory requirements, is presented. It isdesigned for parsimony analysis of data sets comprising many characters formoderate numbers of taxa (in the order of up to a few hundred). The programcan avoid using vast amounts of RAM by temporarily saving data to disk buffers,only parts of which are periodically read back in by the program. In this way, theentire data set is never held in RAM by the program - only small parts of it. Whileusing disk files to store the data slows down searches, it does so only by arelatively small factor (4x to 5x), because the program minimizes the number oftimes the data must be accessed (i.e. read back in) during tree searches. Thus,even if the program is not designed primarily for speed, runtimes are within anorder of magnitude of those of the fastest existing parsimony programs.