[Inparanoid] Analyzing 17 proteome orthology with Inparanoid

[mateusz.kaduk at gmail.com]

Dear Sammy,

There is no script with inparanoid to automate pairwise runs, but I am
using the following code to run all n(n-1)/2 pairwise comparisons without
outgroup, it's just few lines of code, but maybe you will find it useful.

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

# Here is the list of fasta files in the same directory as inparanoid.pl
my @species = ("c_albicans-2011-04i.fa",
               "c_neoformans-2011-04i.fa",
               "s_cerevisiae-2011-04i.fa",
               "s_pombe-2011-04i.fa",
               "y_lipolytica-2011-04i.fa");

my $numberOfspecies = @species;

# Run all n(n-1)/2 combinations without outgroup
for (my $i = 0; $i < $numberOfspecies-1; $i++) {
    for(my $j = $i+1; $j < $numberOfspecies; $j++) {
    print "Staring inparanoid for: ". $species[$i]."\t".$species[$j]."\n";
    system ("./inparanoid.pl ".$species[$i]."\t".$species[$j]."\n");
    }
}

Regards,
Mateusz


On Tue, Oct 7, 2014 at 1:27 PM, Sammy Desilva <sammy.ich17 at gmail.com> wrote:

> Dear Prof. Sonnhammer,
>
> I understand in case of 17 proteome I have to use multiparanoid for
> clustering after computing 17*16/2 = 136 pairs with InParanoid. I wonder is
> any script already available to automate the computations of multiple pairs
> (here 136) with InParanoid for getting input for MultiParanoid?
>
> Regads
> Sammy
>
>
> On Mon, Sep 22, 2014 at 2:33 PM, Erik Sonnhammer <
> erik.sonnhammer at scilifelab.se> wrote:
>
>>  Hi,
>>
>> If you want ortholog groups that include all 17 species, InParanoid won't
>> work. But if you only need pairwise relationships (which is usually the
>> case) then it will.  Then you have to run InParanoid for all 17*16/2 pairs.
>>
>> Erik Sonnhammer
>>
>> On 09/20/2014 11:32 AM, Sammy Desilva wrote:
>>
>>  Hi, I want to assign orthology relationship among 17 proteomes. Could
>> someone please suggest me how to do it offline in Inparanoid? The running
>> command for such cases? I guess putting 3 organism it treats third as
>> outgroup.
>>  Thanks
>>
>>
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