LingPy

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

lingpy.align.multiple.Multiple(seqs, **keywords) Basic class for multiple sequence alignment analyses.
lingpy.align.sca.Alignments(infile[, row, ...]) Class handles Wordlists for the purpose of alignment analyses.
lingpy.align.sca.MSA(infile, **keywords) Basic class for carrying out multiple sequence alignment analyses.
lingpy.align.pairwise.Pairwise(seqs[, seqB]) Basic class for the handling of pairwise sequence alignments (PSA).
lingpy.align.multiple.Multiple.get_pairwise_alignments([...]) Function creates a dictionary of all pairwise alignments scores.
lingpy.align.multiple.Multiple.get_peaks([...]) Calculate the profile score for each column of the alignment.
lingpy.align.multiple.Multiple.get_pid([mode]) Return the Percentage Identity (PID) score of the calculated MSA.
lingpy.align.multiple.Multiple.iterate_all_sequences([...]) Iterative refinement based on a complete realignment of all sequences.
lingpy.align.multiple.Multiple.iterate_clusters(...) Iterative refinement based on a flat cluster analysis of the data.
lingpy.align.multiple.Multiple.iterate_orphans([...]) Iterate over the most divergent sequences in the sample.
lingpy.align.multiple.Multiple.iterate_similar_gap_sites([...]) Iterative refinement based on the Similar Gap Sites heuristic.
lingpy.align.multiple.Multiple.lib_align([...]) Carry out a library-based progressive alignment analysis of the sequences.
lingpy.align.multiple.Multiple.prog_align([...]) Carry out a progressive alignment analysis of the input sequences.
lingpy.align.multiple.Multiple.sum_of_pairs([...]) Calculate the sum-of-pairs score for a given alignment analysis.
lingpy.align.multiple.Multiple.swap_check([...]) Check for possibly swapped sites in the alignment.
lingpy.align.sca.MSA.get_pairwise_alignments([...]) Function creates a dictionary of all pairwise alignments scores.
lingpy.align.sca.MSA.get_peaks([gap_weight]) Calculate the profile score for each column of the alignment.
lingpy.align.sca.MSA.get_pid([mode]) Return the Percentage Identity (PID) score of the calculated MSA.
lingpy.align.sca.MSA.iterate_all_sequences([...]) Iterative refinement based on a complete realignment of all sequences.
lingpy.align.sca.MSA.iterate_clusters(threshold) Iterative refinement based on a flat cluster analysis of the data.
lingpy.align.sca.MSA.iterate_orphans([...]) Iterate over the most divergent sequences in the sample.
lingpy.align.sca.MSA.iterate_similar_gap_sites([...]) Iterative refinement based on the Similar Gap Sites heuristic.
lingpy.align.sca.MSA.lib_align([model, ...]) Carry out a library-based progressive alignment analysis of the sequences.
lingpy.align.sca.MSA.prog_align([model, ...]) Carry out a progressive alignment analysis of the input sequences.
lingpy.align.sca.MSA.sum_of_pairs([...]) Calculate the sum-of-pairs score for a given alignment analysis.
lingpy.align.sca.MSA.swap_check([...]) Check for possibly swapped sites in the alignment.
lingpy.align.pairwise.Pairwise.align([gop, ...]) Align a pair of sequences or multiple sequence pairs.
lingpy.align.sca.PSA.align([gop, scale, ...]) Align a pair of sequences or multiple sequence pairs.
lingpy.align.sca.PSA.output([fileformat, ...]) Write the results of the analyses to a text file.
lingpy.align.sca.SCA(infile, **keywords) Method returns alignment objects depending on input file.
lingpy.align.sca.Alignments.align([method, ...]) Carry out a multiple alignment analysis of the data.
lingpy.align.sca.PSA(infile, **keywords) Basic class for dealing with the pairwise alignment of sequences.

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