Skip to content

Neighbour-joining tree performance #627

@alimanfoo

Description

@alimanfoo

Running the plot_njt() function on larger datasets can take upwards of 20 minutes or more specifically in the stage after the pairwise distances have been computed and during the construction of the neighbour-joining tree..

Perhaps there is an opportunity to accelerate or parallelise the neighbour-joining tree construction. Currently we use the implementation from biotite, which was faster than either BioPython or scikit-bio, but perhaps there is room for further improvement.

We could also at least cache the results of the tree computation so we don't need to rerun it.

Metadata

Metadata

Assignees

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions