[ensembl-dev] Multiple alignment for more than 2 species

[Dazong Zhou]

Hi,

I get problems on multiple sequence alignment for more than 2 species using
the sample code at:
http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html (the
code below "Here is an example script with all of this:").

The sample runs well on default, but fails on adding additional species.
That is to say, the below code works when changing "human:mouse" to
"human:dog" but returns no data when changing to "human:mouse:dog" .


my $species = "human";
my $coord_system = "chromosome";
my $seq_region = "14";
my $seq_region_start = 75000000;
my $seq_region_end = 75010000;
my $alignment_type = "LASTZ_NET";
my $set_of_species = "human:mouse";
my $output_file = undef;
my $output_format = "clustalw";
my $help;

GetOptions(
    "help" => \$help,
    "species=s" => \$species,
    "coord_system=s" => \$coord_system,
    "seq_region=s" => \$seq_region,
    "seq_region_start=i" => \$seq_region_start,
    "seq_region_end=i" => \$seq_region_end,
    "alignment_type=s" => \$alignment_type,
    "set_of_species=s" => \$set_of_species,
    "output_format=s" => \$output_format,
    "output_file=s" => \$output_file);

Thanks,
Hunter
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