cocoatree.msa.filter_sequences

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

Filter sequences

Filter (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_threshold : max proportion of gaps tolerated (default=0.4)

seq_threshold : maximum fraction of gaps per sequence (default 0.2)

Returns

filt_seqs : list of the sequences after filter

remaining_posnumpy.ndarray

remaining positions after filtering

Examples using cocoatree.msa.filter_sequences

Mapping original MSA, filtered MSA, PDB, and sectors

Mapping original MSA, filtered MSA, PDB, and sectors

Mutual information versus SCA

Mutual information versus SCA

Perform full SCA analysis on the S1A serine protease dataset

Perform full SCA analysis on the S1A serine protease dataset