Russell Neches

Since the documentation for DeepVirFinder was released, a new version of h5py has been released that breaks API compatibility with previous versions. This PR updates the documentation to suggest pinning...

It would be cool to be able to initialize new SuchTree objects like this : ```python T1 = SuchTree( '~/data/mytree.tree' ) T2 = SuchTree( 'http://example.com/data/mytree.tree' ) T3 = SuchTree( '(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);'...

Build a permutation test function for individual subsets.

Implement SuchLinkedTree.subset_write(), which should write a tree and a link table for the current subset.

Design a significance test that takes into account multiple subset tests.

Write some tests for SuchLinkedTree.linked_distances().

I should probably post some.

Does not seem to work with v1.1.16

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Icon chooser activates on hotkey, but MarkDown processing does not happen.

Dataset names for NaturalEarthFeature() are not discoverable, implicitly excludes raster datasets

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### Description The `NaturalEarthFeature()` interface takes a name for the dataset field. These names are munged from the filenames on the the [Natural Earth Data](https://www.naturalearthdata.com/) website. These names are not...

When comparing many small genomes, it is not possible to create individual files for each genome. For example, IMG/VR v4.1 contains 5,576,197 viral genomes. It is not possible to create...