Bringing the Pandas DataFrame to phylogenetics.
PhyloPandas provides a Pandas-like interface for reading various sequence formats into DataFrames. This enables easy manipulation of phylogenetic data using familiar Python/Pandas functions. Finally, phylogenetics for humans!
How does it work?¶
Don’t worry, we didn’t reinvent the wheel. PhyloPandas is simply a DataFrame (great for human-accessible data storage) interface on top of Biopython (great for parsing/writing sequence data).
Basic Usage¶
Read sequence file into DataFrame.
import phylopandas as ph
df1 = ph.read_fasta('sequences.fasta')
Write phylopandas.DataFrame data to sequence file.
df1.to_clustal('sequences.clustal')
Convert between two sequence formats.
# Read from fasta.
df = phypd.read_fasta('sequences.fasta')
# Write to phylip.
df.to_phylip('sequences.phy')
See the Cookbook page for more things you can do.
Contributing¶
It’s easy to create new read/write functions and methods for PhyloPandas. If you have a format you’d like to add, please submit PRs! There are many more formats in Biopython that I haven’t had the time to add myself, so please don’t be afraid to add then yourself! I thank you ahead of time!