qcf
: quartet concordance factor estimation¶
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.