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    carp 'Warning: duplicate sequence ids!' unless $ali->has_uniq_ids;

This method does not accept any arguments.

=head2 is_protein

Returns true if any sequence of the Ali looks like a protein. See
L<Bio::MUST::Core::Seq> for the exact test performed on each sequence.

    say 'Your file includes nucleotide sequences' unless $ali->is_protein;

This method does not accept any arguments.

=head2 is_aligned

Returns true if any sequence of the Ali appears to be aligned. See
L<Bio::MUST::Core::Seq> for the exact test performed on each sequence.

If the boolean attribute guessing is not set, always returns false.

    carp 'Warning: file does not look aligned!' unless $ali->is_aligned;

This method does not accept any arguments.

=head2 count_seqs

Returns the number of sequences of the Ali. The alias method C<height> is
provided for convenience.

    my $height = $ali->count_seqs;

This method does not accept any arguments.

=head2 width

Returns the width of the Ali (in characters). If the Ali is not aligned,
returns the length of the longest sequence instead.

To avoid potential bugs due to caching, this method dynamically computes the
Ali width at each call. Moreover, the Ali is always uniformized (see below)
beforehands to ensure accurate width value. Therefore, this method is
expensive and should not be called repeatedly (e.g., in a loop condition).

    # you'd better looping through sites like this...
    my $width = $ali->width;
    for my $site (0..$width-1) {
        ...
    }

This method does not accept any arguments.

=head2 seq_len_stats

Returns a list of 5 values summarizing the Ali seq lengths (ignoring gaps).
The values are the following: Q0 (min), Q1, Q2 (median), Q3, and Q4 (max).

This method does not accept any arguments.

=head2 perc_miss

Returns the percentage of missing (and gap-like) character states in the Ali.

As this method internally calls C<Ali::width>, the remarks above also apply.

    my $miss_level = $ali->perc_miss;

This method does not accept any arguments.

=head1 MUTATORS

=head2 uc_seqs

Turn all the sequences of the Ali to uppercase and returns it.

This method does not accept any arguments.

=head2 recode_seqs

Recode all the sequences of the Ali and returns it.

    use aliased 'Bio::MUST::Core::Ali';
    my $ali = Ali->load('biased.ali');

    # set up RY recoding for suppressing codon bias
    my %base_for = (
        A => 'A',   G => 'A',       # purines
        C => 'C',   T => 'C',       # pyrimidines
    );

    my $ali_rec = $ali->recode_seqs( \%base_for );
    $ali_rec->store('biased_ry.ali');

This method requires one argument.

=head2 degap_seqs

Remove the gaps in all the sequences of the Ali and returns it.

This method does not accept any arguments.

=head2 spacify_seqs

Spacifies all the sequences of the Ali and returns it. See the corresponding
method in L<Bio::MUST::Core::Seq> for the exact effect of this gap-cleaning
operation.

This method does not accept any arguments.

=head2 gapify_seqs

Gapifies all the sequences of the Ali and returns it. See the corresponding
method in L<Bio::MUST::Core::Seq> for the exact effect of this gap-cleaning
operation.

This method accepts an optional argument.

=head2 trim_seqs

Trims all the sequences of the Ali and returns it. See the corresponding
method in L<Bio::MUST::Core::Seq> for the exact effect of this gap-cleaning
operation.