(DBA table_five)
Experimental library for quick quintet tallying, useful when you have a lot of quintets that somehow you don't want to count yourself.
Binary wheels are provided on PyPI
python3 -m pip install table_five
TreeSetA treeset is an efficient (i.e., fast parsing) list of tree topologies. The construction is $O(k n \lg n)$ where $k$ is the number of trees and $n$ the number of taxa due to the LCA data structure initialization.
from table_five import TreeSet
trees = TreeSet("path_to_newline_delimited_newicks.tre")
The major API is tally_sinlge_quintet returning a list of length 15 containing the empirical
counts of the 15 ADR unrooted quintet topology among the tree-set in $O(k)$ time:
# get counts of the ADR unrooted quintet topologies on taxa '1','2','3','4','5'. Taxa order matters.
treeset.tally_single_quintet(('1','2','3','4','5'))
# obviously you might want to convert it to numpy arrays
# normalize by the number of genes in the tree-set
new_tree_dist = np.asarray(treeset.tally_single_quintet(q_taxa)) / len(treeset)
FAQs
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We found that table-five demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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