In which we explore the ill-defined and undocumented: In BioRuby, alignments are equipped with several methods for obtaining consensus sequences. Unfortunately, these have terse descriptions which point you at the BioPerl documentation, with the added bon

alignment.rb

# For demonstration purposes,  let's create a very simple alignment, where
# everything agrees xcept the last sequence which leads with a differing
# character and ends with a gap:

require 'bio'
aln = Bio::Alignment.new(['acgt', 'acgt', 'acgt', 'ccg-'])

# consensus_iupac produces a "true" consensus sequence across all members.
# If sequences differ, the consensus sequence has an ambiguous character
# that sums these differences:

print aln.consensus_iupac()   # "mcg?"

# Note the first position is m (a or c), but where gaps exist, like the final
# position, the final character is marked gnomically as ?.

# An extra complication is the handling of gaps. The option :gap_mode
# takes the values 0, 1 or -1, which correspond to treating gaps like a
# character (the default), any gaps at that site appearing in the output
# (i.e. effectively stripping no-gap characters) and stripping all gaps
# before calculating the consensus:

print aln.consensus_iupac(:gap_mode=>0)    # "mcg?"
print aln.consensus_iupac(:gap_mode=>1)    # "mcg-"
print aln.consensus_iupac(:gap_mode=>-1)   # "mcgt"

# consensus_string uses a threshold to calculate the consensus character
# at that site: if the most frequent residue meets the threshold, it is
# selected. Gap characters are treated as above:

print aln.consensus_string(threshold=0.5)                            # "acgt"
print aln.consensus_string(threshold=0.5, :gap_mode=>0)     # "acgt"
print aln.consensus_string(threshold=0.5, :gap_mode=>1)     # "acg-"
print aln.consensus_string(threshold=0.5, :gap_mode=>-1)    # "acgt"