cons2seqs_sim: Group consensus to each sequence in the alignment similarity
In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description Usage Arguments Details Value Examples

The function calculates similarity of group consensus to each sequence in the alignment. It facilitates an assessment of consensus accuracy and identification of outlying sequences in the alignment. Grouping amino acids allows to check similiarity between sequences by amino acids properties of user's choice.

1	cons2seqs_sim(grouped_alignment, grouped_consensus_seq)

`grouped_alignment`	The output of `read.alignment` function
`grouped_consensus_seq`	A string of amino acids, the output of `consensus` function

AA in consensus sequences and aligned sequences are converted into groups symbols according to method of user's choice. Returned values are percentage of similar amino acids considering the properties in consensus sequence and aligned sequence.

numeric vector of identity score (percentage); positions in the numeric vector correspond to sequences in alignment, respectively

data("small_alignment")
alignment = delete_isoforms(small_alignment)
threshold_consensus = 30
grouping_method = "substitution_matrix"
alignment_grouped = align_seq_mtx2grs(alignment2matrix(alignment),grouping_method)
consensus_seq_grouped = consensus(alignment_grouped, threshold_consensus)
consensus_to_seqs_similarity = cons2seqs_sim(alignment_grouped, consensus_seq_grouped)