To extract consensus in UGENE with the command line interface you need to use UGENE Workflow Designer. There is an element that extracts consensus from each input alignment. You can create a workflow that reads alignment, extracts consensus and output consensus sequences to files. Since any workflow can be run from command line that's exactly what you need. Actually, you can find the pre-built workflow in the Samples bar of the Workflow Designer.

• Workflow Designer docs
• Running workflows from command line

So it will be something like: ugenecl --task=extract_consensus --in=in.aln --out=out.fa

P.S. These functions will be released only in UGENE 1.14, that it why you did not find it in the documentation. But to get them right now, you can use the development snapshot from here

The program phrophecy of EMBOSS package should do it.

An example of an EMBOSS server can be found here, you can download and install it locally using command line.

I wrote this perl script to take in a fasta alignment and output a full IUPAC consensus and also list 50 probes of X size which are weighted for A/C/T/G. It might help:

Usage is:

./degenerate_code_generator alignment_file.fasta window_size outfile.txt

#!/usr/bin/perl
use strict;
use warnings;

use Bio::Seq;
use Bio::AlignIO;
use Bio::Tools::IUPAC;

my $usage = "USAGE:\t./degenerate_code_generator REFERENCE_FILE.fasta Probe_size OUTFILE.txt\n";

my $infile = $ARGV[0] or die $usage . "\n";
my $probesize = $ARGV[1] or die $usage . "\n";
my $outfile = $ARGV[2] or die $usage . "\n";

my $alnio = Bio::AlignIO->new(-file => $infile, -format => 'fasta');

open OUTFILE, ">$outfile";
select OUTFILE;

my $cs;

while (my $aln = $alnio->next_aln) {
    $cs = $aln->consensus_iupac;
    my $seq = Bio::Seq->new(-seq => $cs, -alphabet => 'dna');
}

$cs =~ s/-//g;
print "<FULL>$cs\n";

my $score;

my $winsize = $probesize;
my $i = 1;
my $cs_len = length($cs);
my %hash;

while ($i < $cs_len) {
        my $window = substr($cs, $i,$winsize);
        $i++;

        foreach (split(//,$window)){
                if(m/A|C|T|G|U/){
                        $score += "5";
                }elsif(m/R|Y|S|W|K|M/){
                        $score += "1";
                }
        }
        $hash{$window} = $score;
        $score = 0;
}

my @keys = sort { $hash{$b} <=> $hash{$a} } keys(%hash);
my @vals = @hash{@keys};

my $c = 0;

#print "Score\tProbe\n";

while ($c < 51){
        print "$vals[$c]\t$keys[$c]\n";
        $c++;
}