cocoatree.msa.filter_sequences¶

cocoatree.msa.filter_sequences(sequences, sequences_id, gap_threshold=0.4, seq_threshold=0.2, verbose=False)[source]¶

Filter sequences

Remove (1) overly gapped positions; (2) overly gapped sequences.

Parameters¶

sequences : list of MSA sequences to filter

sequences_id : list of the MSA’s sequence identifiers

gap_thresholdfloat,: maximum proportion of gaps tolerated per position (default=0.4)
seq_thresholdfloat,: maximum proportion of gaps tolerated per sequence (default=0.2)

filtered_seqslist of the remaining sequences (written as strings): after applying the filters
filtered_seqs_idlist of sequence identifiers that were kept after: applying the filters
remaining_posnumpy.ndarray: remaining positions after filtering