GARLI: genetic algorithm for rapid likelihood inference. GARLI performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites. The implementation of this model is exactly equivalent to that in PAUP* (by David Swofford), so that likelihood scores obtained by each program are directly comparable. Besides the OS X GUI version, GARLI is not interactive. All program settings are specified in a configuration file. Examples come with the program, and the manual describes all of the options. The program reads non-interleaved phylip and nexus datafiles. In reality it is not currently very nexus compliant, and can be confused in various ways. It should have no problem with nexus datasets exported directly from PAUP, however. GARLI also implements a parallel MPI based algorithm for use on parallel computing clusters (note that the parallel version seeks to perform a more thorough tree search and does NOT reduce runtimes. It typically is only helpful on datasets with greater than about 500 sequences)

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  1. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)