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## alignment.compare_with() -- compare two alignments

`compare_with(aln)`

> This command compares two pairwise alignments read by the alignment.append() commands. The alignment of the first sequence with the second sequence in ALIGNMENT is evaluated with respect to `'aln'`. The numbers are not symmetric; i.e., they will change if the sequences or alignments are swapped. The output in the `log` file is self-explanatory.

Example: examples/commands/compare_alignments.py

      # Example for: alignment.compare_with(), alignment.append_model()

      # Compare two alignments of two proteins each. In this case, the first
      # alignment is a sequence-sequence alignment and the second alignment
      # is a structure-structure alignment.

      from modeller import *
      log.level(1, 1, 1, 1, 0)
      env = environ()
      env.io.atom_files_directory = '../atom_files'

      # Generate and save sequence-sequence alignment:
      aln = alignment(env)
      for code in ('1fas', '2ctx'):
          mdl = model(env, file=code)
          aln.append_model(mdl=mdl, align_codes=code, atom_files=code)
      aln.align(gap_penalties_1d=(-600, -400))
      aln.write(file='toxin-seq.ali')

      # Generate and save structure-structure alignment:
      aln.align3d(gap_penalties_3d=(0, 2.0))
      aln.write(file='toxin-str.ali')

      # Compare the two pairwise alignments:
      aln  = alignment(env, file='toxin-seq.ali', align_codes='all')
      aln2 = alignment(env, file='toxin-str.ali', align_codes='all')
      aln.compare_with(aln2)