phylopandas

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Fix Bio.Alphabet import error

3

Remove all Bio.Alphabet occurrences due to official documentation https://biopython.org/wiki/Alphabet.

VectorVP

Bio.Alphabet removed from Biopython

4

`import phylopandas as ph` raises error ```python --------------------------------------------------------------------------- ImportError Traceback (most recent call last) in ----> 1 import phylopandas as ph ~/anaconda3/envs/covid/lib/python3.8/site-packages/phylopandas/__init__.py in 26 27 # Register PhyloPandas Methods --->...

maxdevblock

Add tree pruning method

1

Adds a `.phylo.prune()` method. The function takes a simple kwarg. The key is the column name in the DataFrame and the value is row's value at that column. ## Example:...

Zsailer

Add MSA sub-dataframe to main dataframes.

1

@harmsm and @jharman25 will be interested. Here's a method that enables you to access sequence data from a phylopandas dataframe as its own sub-dataframe. You can visualize, slice, and analyze...

Zsailer

Include all dependencies in `requirements.txt`

1

pytest

safay

Added a clustal test file, an example notebook, and alignment parsing…

3

… in the _read function. Also made two hidden funcitons to iterate sequence and alignment biopython objects. Did a bit of hacking to get the dataframes to have the same...

biophyser