qcf: quartet concordance factor estimation

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qcf is a C++ program for estimating quartet concordance factors from multilocus sequence data. It uses the LogDet transformation to calculate the frequency of gene tree quartets matching the three possible unrooted species tree topologies for a set of four taxa. qcf can handle multiple haplotypes per taxon/population, and outputs a CSV file that can be used to infer a species tree using scripts from the TICR pipeline and is compatible with the SNaQ method for phylogenetic network inference implemented in the Julia package PhyloNetworks.

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