ghost-tree

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Improve taxonomy line issues in files (i.e. allow taxonomy to be in different locations)

1

Sometimes the taxonomy is in different locations or another file. Allow people to add a taxonomy file instead of requiring that the fasta file (foundation) contains all the taxonomy. ghost-tree...

JTFouquier

Might be nice to add this as a feature in the future.

JTFouquier

Add option for user to scale branch lengths

4

JTFouquier

write script to automate tree building

JTFouquier

Improve code complexity in ghosttree.scaffold

1

Suggestion from D.M.: line 102, which determines which sequences to write out, is performing a list look up. This can be reduced to O(1). It is also not using the...

JTFouquier

See reference emails and script attachments

JTFouquier

This script works, but it's awful to have a user open the file and add their ghost-tree! Need to fix this!

JTFouquier

Test quality of the trees using the alpha release (from paper) as a control prior to building multiple trees from the new Silva release as a foundation tree.

JTFouquier

Try adding a Click progress bar (for large files ghost-tree takes some time)

1

via Click http://click.pocoo.org/4/utils/

JTFouquier

perform filter high entropy positions and gap positions to tree prior to extending... @gregcaporaso I was under the impression that this step was important specifically for trees with excessively long...

JTFouquier