LinTInd - Lineage tracing by indels
When we combine gene-editing technology and sequencing
technology, we need to reconstruct a lineage tree from alleles
generated and calculate the similarity between each pair of
groups. FindIndel() and IndelForm() function will help you
align each read to reference sequence and generate scar form
strings respectively. IndelIdents() function will help you to
define a scar form for each cell or read. IndelPlot() function
will help you to visualize the distribution of deletion and
insertion. TagProcess() function will help you to extract
indels for each cell or read. TagDist() function will help you
to calculate the similarity between each pair of groups across
the indwells they contain. BuildTree() function will help you
to reconstruct a tree. PlotTree() function will help you to
visualize the tree.