Given a tree topology (newick format), a set of reference sequence names defining clades of interest in the tree topology, and a FASTA file containing all sequences represented in the tree, this simple Python script generates an individual FASTA file for sequences contained in each of the clades. This involves use of the Environment for Tree Exploration (ETE3) to find the most inclusive clade containing each reference sequence, but no other reference sequences. The names of sequences in each clade are then copied from the complete FASTA file to a clade-specific FASTA file in a given output directory path.
Activate a conda environment from the environment definition file
(sort_seqs_by_clade_conda_env.yaml).
python3 sort_seqs_by_clade.py <topology file in newick format> \
<file listing reference sequence names> \
<fasta file with all sequences> \
<path to output directory to be generated>