LingPy

This documentation is for version 2.0.dev, which is not released yet.

lingpy.align.multiple.Multiple

class lingpy.align.multiple.Multiple(seqs, **keywords)

Basic class for multiple sequence alignment analyses.

Parameters :

seqs : list

List of sequences that shall be aligned.

Notes

Depending on the structure of the sequences, further keywords can be specified that manage how the items get tokenized.

Methods

get_pairwise_alignments([new_calc, model, ...]) Function creates a dictionary of all pairwise alignments scores.
get_peaks([gap_weight]) Calculate the profile score for each column of the alignment.
get_pid([mode]) Return the Percentage Identity (PID) score of the calculated MSA.
iterate_all_sequences([check, mode, gop, ...]) Iterative refinement based on a complete realignment of all sequences.
iterate_clusters(threshold[, check, mode, ...]) Iterative refinement based on a flat cluster analysis of the data.
iterate_orphans([check, mode, gop, scale, ...]) Iterate over the most divergent sequences in the sample.
iterate_similar_gap_sites([check, mode, ...]) Iterative refinement based on the Similar Gap Sites heuristic.
lib_align([model, mode, modes, scale, ...]) Carry out a library-based progressive alignment analysis of the sequences.
prog_align([model, mode, gop, scale, ...]) Carry out a progressive alignment analysis of the input sequences.
sum_of_pairs([alm_matrix, mat, gap_weight, gop]) Calculate the sum-of-pairs score for a given alignment analysis.
swap_check([swap_penalty, score_mode]) Check for possibly swapped sites in the alignment.

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