Cookbook

Merge two sequence files

Use pandas.concat to merge two sequence files.

import phylopandas as ph

seq1 = ph.read_fasta('seq1.fasta')
seq2 = ph.read_fasta('seq2.fasta')

# Merge two files
seqs = seq1.concat(seq2, ignore_index=False)

# Write to file.
seqs.to_fasta('seqs.fasta')

Merge alignment and sequence data

Add alignment column to sequence DataFrame.

import phylopandas as ph

# Read sequences and alignments.
seq = ph.read_fasta('sequences.fasta')
ali = ph.read_fasta('alignment.fasta')

# Merge data.
seq.merge(ali, on='id')