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. |