The GroupAcc includes two pooling-based phylogenetic approaches with improved statistical power to infer weakly accelerated evolution. The key idea of GroupAcc is to group TFBSs by the bound transcription factor and then examine whether each TFBS group as a whole shows an elevated substitution rate in a lineage of interest.
The GroupAcc is implemented in R with several packages.
X.zip: a zip directory composed of alignments of specific group of genetic elements
ref_trimmed.RData: a reference phylogenetic model file in the format of RData
tfbs_n1_nogap.nh: a reference phylogenetic tree containing the topology
hg19: the lineage of interest
mkdir groupLRT_output/
Rscript groupLRT.R ZZZ3.zip ref_trimmed.RData tfbs_n1_nogap.nh hg19 groupLRT_output/ > groupLRT_output/hg19_groupLRT.txt
mkdir mixSingle_output/
Rscript mixSingle.R POU5F1/ ref_trimmed.RData tfbs_n1_nogap.nh hg19,panTro2 mixSingle_output/ > mixSingle_output/mixSingle.txt