alifedata-phyloinformatics-convert

alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data

• Free software: MIT license
• Documentation: https://alifedata-phyloinformatics-convert.readthedocs.io.

Built using the dendropy library.

Use it as a command line tool to convert to alife standard phylogenetics data

Usage: alifedata-phyloinformatics-convert toalifedata [OPTIONS]

  convert standard alife phylogeny data to phloinformatics format

Options:
  --input-file FILENAME   phyloinformatics data file path; default stdin
  --input-schema TEXT     phyloinformatics data format schema; options include
                          newick, nexml, and nexus  [required]
  --output-file FILENAME  alife data file path; default stdout
  --output-format TEXT    alife data file format; default csv
  --help                  Show this message and exit.

Use it as a command line tool to convert from alife standard phylogenetics data

Usage: alifedata-phyloinformatics-convert fromalifedata [OPTIONS]

  convert phloinformatics data to standard alife phylogeny format

Options:
  --input-file FILENAME   alife data file path; default stdin
  --input-format TEXT     alife data file format; default csv
  --output-file FILENAME  phyloinformatics data file path; default stdout
  --output-schema TEXT    phyloinformatics data format schema; options include
                          newick, nexml, and nexus  [required]
  --help                  Show this message and exit.

Use it as a Python module

import alifedata_phyloinformatics_convert as apc

alife_df = pd.read_csv('alifedata.csv')


# get a dendropy Tree from alife-standardized phylogeny pandas dataframe
dendropy_tree = apc.alife_dataframe_to_dendropy_tree(alife_df)

# get a alife-standardized phylogeny pandas dataframe from a dendropy Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(dendropy_tree)


# get a biopython Tree from alife-standardized phylogeny pandas dataframe
biopython_tree = apc.alife_dataframe_to_biopython_tree(alife_df)

# get a alife-standardized phylogeny pandas dataframe from a biopython Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(biopython_tree)

# get a networkx DiGraph from alife-standardized phylogeny pandas dataframe
networkx_digraph = apc.alife_dataframe_to_networkx_digraph(alife_df)

# get adjacency lists from alife-standardized phylogeny pandas dataframe
adjjacency_lists = apc.alife_dataframe_to_dict_of_lists(alife_df)

Install from PyPi

pip3 install alifedata-phyloinformatics-convert

Citing

If alifedata-phyloinformatics-convert is used in scientific publication, please cite it as

Matthew Andres Moreno and Santiago Rodriguez Papa. (2024). mmore500/alifedata-phyloinformatics-convert. Zenodo. https://doi.org/10.5281/zenodo.10701178

@software{moreno2024apc,
  author = {Matthew Andres Moreno AND Santiago Rodriguez Papa},
  title = {mmore500/alifedata-phyloinformatics-convert},
  month = feb,
  year = 2024,
  publisher = {Zenodo},
  doi = {10.5281/zenodo.10701178},
  url = {https://doi.org/10.5281/zenodo.10701178}
}

And don't forget to leave a star on GitHub!

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.