--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP-1.2.1/multiparanoid.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,728 @@
+#!/usr/bin/perl
+#
+# Copyright (C) Andrey Alexeyenko and Erik Sonnhammer, 2006
+# For a license to use this program, contact Erik.Sonnhammer@cbc.su.se
+###############################################################################
+# Andrey Alexeyenko, Stockholm Bioinformatics Center, Albanova, Stockholm 2006
+# mailto:avalex99@mail.ru
+###############################################################################
+# The program is a postprocessor of ortholog tables produced by InParanoid. It combines pairwise InParanoid outputs (say, A-B, B-C, A-C) and makes multi-species clusters of orthologs ABC. 
+
+use strict vars;
+use DBI;
+use Cwd;
+require 5.002;
+
+our($inputdir, $makeunique,  $indirect, $Pair, 
+@fields, @cutoffs, $output, @fields_out, $out, $algo, $debug, $SQLprefix, 
+%place, $nplaces, $source_by_cluster, $source_by_gene, $source_by_taken, $seeds, $use_bootstrap, $maxINPscore, $toMainOrthologOfSelf);
+my($npairs, $i, $j, $ii, $ee, $gg, $nn, $oo, $s2, $s1, $nspec, $as, $newmain, @distances, @species, $sp1, $sp2, $clusno, $specletters, $a_pair, $a_cluster, $pms, $input, $output, $inputfile, $new, $thepair);
+###############################################################################
+
+#FIRST OF ALL, set the variables $inputdir  and $output below. MultiParanoid may not work without it!!!
+
+#Parameters to submit (may be abbreviated to the first letter):
+# OBLIGATORY:
+# -species: a list of several species connected with "+"; e.g. mouse+cat+dog; names of the genomes exactly how they are called both in file names and inside of files. NOTE: due to phylogenetic tree conflicts, order of the genomes slightly changes the result. The input files (the InParanoid output) should thus be called:
+# sqltable.dog-cat, sqltable.dog-mouse etc. 
+#To use other file names, one should change the variable $SQLprefix below.
+
+# OPTIONAL:
+# -cutoff: deprecated. But one can use it to tighten the clusters (to filter out weaker in paralogs by restricting with the distance to the seed orthologs); Example: " -cutoff 0.5 " or, for doing 3 different cluster versions at the same time: 0+0.2+0.5. Default: 0 (no cutoff). 
+# -algo: how to define between-paralogs distances while clustering. 
+#              Options: onlymains (default and only reasonable)
+#                       toallsorted
+# -debug: 0 or 1; default: 0
+# -input: deprecated, now defined by -species parameter, and the input files shall have conventional names
+# -output: deprecated, special message will tell the name of the output file 
+# -unique: 0 or 1; set to 1, if the duplicates (genes clustered twice) should be removed; default: 0
+
+#The MultiParanoid output header:
+### clusterID       species gene    is_seed_ortholog        confidence_score        species_in_cluster      tree_conflict###
+
+#is (hopefully) self-explanatory. Though:
+
+# "is_seed_ortholog" means the protein was a seed ortholog in at least one InParanoid cluster.
+# "confidence_score" is an average InParanoid score across the input clusters 
+# "tree_conflict" indicates that, from the point of view of different species, the number of inparalogs varied in at least one other species ("diff.numbers") or the numbers were the same, but the IDs differed ("diff.names"). 
+
+#NOTE: s.c. 'distances' between cluster members are, in fact, similarities. Variables are called 'distances' for historical reasons. 
+# 'main orthologs' (defined by InParanoid) are better to be called 'seed orthologs'.  
+
+# Settings:    
+
+$algo 		= 'onlymains';
+$debug 		= 0;
+$use_bootstrap = 0;
+$maxINPscore = 1;
+$toMainOrthologOfSelf = 0;
+$indirect = 1; #this option allows using the currently default InParanoid output, were seed orthologs are recognized by the feature "IPscore = 1.00". Otherwise ($indirect = 0) a special format should be used (needs a change in the InParanoid script and is now deprecated).
+
+if ($indirect) {
+$SQLprefix = 'sqltable.';
+$inputdir = './'; #change it respectively
+$place{'clusterID'} 	= 0; #these should correspond to the current InParanoid output format
+$place{'BLASTscore'} 	= 1;
+$place{'species'} 		= 2;
+$place{'IPscore'} 		= 3;
+$place{'gene'} 			= 4;
+$place{'main'} 		= 5;
+$place{'pair'} 			= 6;
+}
+else {
+$SQLprefix = 'ava_sql';
+$inputdir = 'disk/dir/multiparanoid/';  #change it respectively
+###The older, ava_sql, version:
+$place{'clusterID'} 	= 0;
+$place{'BLASTscore'} 	= 1;
+$place{'pair'} 			= 2;
+$place{'species'} 		= 3;
+$place{'gene'} 			= 4;
+$place{'IPscore'} 		= 5;
+$place{'main'} 		= 6;
+#$indirect = 1 if !defined($place{'main'});
+}
+
+$pms = parseParameters(join(' ', @ARGV));
+if (!$pms->{'s'}) {die "No '+'-delimited input species list (pointing to INPARANOID output) specified. Check parameter '-species'... ";}
+@species 	= split(/\+/, $pms->{'s'});	#list of species (genomes) as they appear in the file names. Default: no default
+print "Species list: $pms->{'s'}\n is treated as species ".join(', ', @species)."\n";
+#print "Genomes @species are being processed...\n";
+$makeunique = 0;#also, mind the variables $inputdir  and $output below
+$makeunique = $pms->{'u'};
+
+$specletters = fstLetters(@species);
+# $output = 'diskZ/MultiparanoidOuput/'.$specletters.'.MP.sql' if !$output; #change it respectively
+
+$output = './MP.Cluster' ; #change it respectively
+
+
+@cutoffs = split(/\+/, $pms->{'c'});	#Can restrict included in-paralogs by their distance to the main ones (see example below). Default: 0 (no cutooff)
+#@cutoffs = (0, 0.25, 0.5, 0.75, 1);
+@cutoffs = (0) if !exists($cutoffs[0]);
+
+$algo 		= $pms->{'a'} if !$algo;	#which algorithm to use. Default: onlymains
+$debug 		= $pms->{'d'};	#degree of debug messages' output. Default: no
+$output = $pms->{'o'} if !$output;
+$makeunique = $pms->{'u'} if !$makeunique;
+
+$nplaces = scalar(keys(%place));
+@fields_out = (clusterID, species, gene, is_seed_ortholog, confidence_score, species_in_cluster, tree_conflict);
+push @fields_out, 'cutoff' if scalar(@cutoffs) > 1;
+$nspec = scalar(@species);
+open OUT, ">$output";
+
+print "Genome pairs found and used: \n"  if $debug > 0;
+for ($s1 = 0; $s1 < $nspec; $s1++) {
+for ($s2 = 0; $s2 < $nspec; $s2++) {
+           next if ($species[$s1] eq $species[$s2]);
+$Pair = $species[$s1].'-'.$species[$s2];
+$inputfile = $inputdir.$SQLprefix.$Pair;
+if (!system("ls $inputfile")) {
+loadData($inputfile);
+$npairs++;
+}}}
+die "Not enough (or too many) species pair files for ".join(", ", @species)."\n" if $npairs !=  ($nspec * ($nspec - 1)) / 2;
+$clusno = 1;
+
+for $sp1(@species) {
+for $sp2(@species) {
+$thepair = "$sp1-$sp2";
+
+next if (!$source_by_cluster->{$thepair} or ($sp1 eq $sp2));
+print "Analyzing $sp1 vs. $sp2: " if $debug;
+print scalar(keys(%{$source_by_cluster->{$thepair}}))." clusters for this pair...\n" if $debug;
+for $a_cluster(keys(%{$source_by_cluster->{$thepair}})) {
+undef $new; undef $seeds;
+$seeds = findOrthos($a_cluster, $thepair);
+
+#find recordset of orthologs of the both species (for cluster a) from the pairwise subset i-j
+next if !defined($seeds->[0]);
+LINE1:for $gg(@{$seeds}) {
+next if (!$gg->[$place{'main'}] or $gg->[$nplaces]);
+$gg->[$nplaces] = 1;
+for $a_pair(keys(%{$source_by_cluster})) {
+if (($a_pair =~ $gg->[$place{'species'}]) and ($gg->[$place{'pair'}] ne $a_pair)) {
+$new = findNewOrtho($gg->[$place{'gene'}], $a_pair);
+undef $newmain;
+if (defined($new)) {
+for $nn(@{$new}) {
+push(@{$seeds}, $nn) if isNew($seeds, $nn);
+$newmain = 1 if $nn->[$place{'main'}];
+}
+redo LINE1 if $newmain;
+}}}}
+
+makeClusters($seeds, \@cutoffs, \@species, $clusno++, treeConflict($seeds), $specletters);
+}}}
+if ($clusno > 20) {
+print OUT join("\t", @fields_out)."\n";
+for $oo(@{$out->{'byRecord'}}) {
+print OUT join("\t", @{$oo})."\n" if defined($oo);
+}
+print "Making ortholog clusters of ".join(', ', @species)." done. The result is in file $output\n";
+}
+else {
+die "No output has been produced..."
+}
+###########################################################################
+
+sub parseParameters {
+my($parameters) = @_;
+my($key, $value, $pars, %pars);
+
+#print "$parameters\n";
+$_ = $parameters;
+ while (m/\-(\w+)\s+([a-zA-Z0-9._=+]+)/g) {
+next if ((lc($2) eq 'f') or (lc($2) eq 'false') or (lc($2) eq 'no') or (lc($2) eq '0'));
+$pars{substr($1, 0, 1)} = $2;
+}
+if (scalar(keys(%pars)) < 1 or !$pars{'s'} or m/\-h/) {
+print "\nNOT ENOUGH PARAMETERS!\nOBLIGATORY:
+-species: a list of several species connected with '+'; e.g. mouse+cat+dog; names of the genomes exactly how they are called both in file names and inside of files. NOTE: due to phylogenetic tree conflicts, order of the genomes slightly changes the result. The input files (the InParanoid output) should thus be called:
+sqltable.dog-cat, sqltable.dog-mouse etc. 
+To use other file names, one should change the variable \$SQLprefix inside the scrtipt.
+\nOPTIONAL:
+\n-cutoff: deprecated. But one can use it to tighten the clusters (to filter out weaker in paralogs by restricting with the distance to the seed orthologs); Example: ' -cutoff 0.5 ' or, for doing 3 different cluster versions at the same time: 0+0.2+0.5. Default: 0 (no cutoff). 
+\n-algo: how to define between-paralogs distances while clustering. 
+              Options: onlymains (default and only reasonable)
+                       toallsorted
+\n-debug: 0 or 1; default: 0
+\n-input: deprecated, now defined by -species parameter and the variables \$inputdir and \$SQLprefix, and the input files shall have conventional names
+\n-output: deprecated, special message will tell the name of the output file 
+\n-unique: 0 or 1; set to '0' if the duplicates (genes clustered twice) should BE REMOVED, to '1' otherwise; default: 0\n\n"; exit;
+}
+while (($key, $value) = each(%pars)) {
+print "Parameter $key = $value;\n";
+}
+
+return(\%pars);
+}
+
+sub treeConflict { #tells if there is a discrepancy, for species B, between 2-species trees A-B and B-C 
+my($seeds) = @_;
+my($i, $ii, $jj, $kk, $sets);
+
+for $ii(@{$seeds}) {
+push @{$sets->{$ii->[$place{'species'}]}->{$ii->[$place{'pair'}]}}, $ii->[$place{'gene'}];
+}
+
+for $ii(keys(%{$sets})) {
+for $jj(keys(%{$sets->{$ii}})) {
+for $kk(keys(%{$sets->{$ii}})) {
+next if $jj eq $kk;
+if (scalar(@{$sets->{$ii}->{$jj}}) != scalar(@{$sets->{$ii}->{$kk}})) {return('diff. numbers');}
+sort {$a <=> $b} @{$jj};
+sort {$a <=> $b} @{$kk};
+for ($i = 0; $i < scalar(@{$sets->{$ii}->{$jj}}); $i++) {
+if ($sets->{$ii}->{$jj}->[$i] ne $sets->{$ii}->{$kk}->[$i]) {
+return('diff. names');
+}}}}}
+return(undef);
+}
+
+sub makeClusters {
+my($seeds, $cutoffs, $species, $clusno, $conflict, $param) = @_;
+my($clo, $le, $gg, @included, $distances, $specset, $cco);
+
+array2StdOut($seeds, "Primers") if $debug;
+if ($algo eq 'onlymains') {
+$distances = pairWiseDist2Main($seeds);
+}
+elsif ($algo eq 'toallsorted') {
+$distances = pairWiseDist2All($seeds);
+}
+else {die "Algorithm is not set...";}
+array2StdOut(setUnique($seeds), "Unique") if $debug;
+for $cco(@{$cutoffs}) {
+undef @included;
+
+@included = firstMains($seeds);
+@included = @{setUnique(\@included)} if defined(@included);
+array2StdOut(\@included, 'Mains') if $debug;
+goto LINE3 if $cco == 1; 
+
+if ($algo eq 'onlymains') 		{
+push @included, @{getOthers(
+								setUnique($seeds),
+								$distances,
+								\@included,
+								$cco)};
+}
+elsif ($algo eq 'toallsorted') 	{
+@included 	=  	@{getClosests(
+								setUnique($seeds),
+								$distances,
+								\@included,
+								$cco)};}
+LINE3:array2StdOut(\@included, "Cluster with cut-off $cco") if $debug;
+LINE4: $specset = join('', fstLetters(sort(listSpecies(\@included, $species))));
+$conflict = (($conflict) ? $conflict : 'No');
+for $gg(@included) {
+next if $makeunique and alreadyClustered($gg, $cco); 
+$ii = scalar(@{$out->{'byRecord'}});
+$out->{'byName'}->{$gg->[$place{'gene'}]}->{$cco} = $ii;
+
+for $ee($clusno, 
+	$gg->[$place{'species'}], 
+	$gg->[$place{'gene'}], 
+	$gg->[$place{'main'}], 
+	$gg->[$place{'IPscore'}], 
+	$specset, 
+	$conflict) {push @{$out->{'byRecord'}->[$ii]}, $ee;}
+push @{$out->{'byRecord'}->[$ii]}, $cco if scalar(@cutoffs) > 1;
+
+}
+#$out .=  join("\t", (100 * $cco, $clusno, $gg->[$place{'species'}], $gg->[$place{'gene'}], $gg->[$place{'main'}], $gg->[$place{'IPscore'}], $specset, $conflict, $param, $algo))."\n" if !$makeunique or !alreadyClustered($gg);
+}
+return;
+}
+
+
+sub fstLetters {
+my(@list) = @_;
+my($letters, $ii, $firstLetter, $lastLetter);
+
+return(join('-', sort {$a cmp $b} @list));
+$firstLetter = 0; 
+for $ii(@list) {
+$lastLetter = length($ii) - $firstLetter;
+$letters .= "_".substr($ii, $firstLetter, $lastLetter);
+}
+
+return $letters;
+}
+
+sub listSpecies {
+my($ar, $species) = @_;
+my($already, %already, $ii, @flags);
+# checks for species present in the current cluster
+
+for $ii(@{$ar}) {
+push(@flags, $ii->[$place{'species'}]) if !$already{$ii->[$place{'species'}]};
+$already{$ii->[$place{'species'}]} = 1;
+}
+return(@flags);
+}
+
+sub loadData {
+my($inputfile) = @_;
+my($line, @line, $i);
+
+open(IN, $inputfile);
+print "Loading $inputfile...\n";
+while (<IN>) {
+@line = split /\s+/;
+#$place{'BLASTscore'}, $place{'species'}, $place{'IPscore'}, $place{'main'}
+for $i(0..scalar(keys(%place))) {
+if ($indirect) {
+if ($i == $place{'main'}) {
+$source_by_cluster->{$indirect ? $Pair : $line[$place{'pair'}]}->{$line[$place{'clusterID'}]}->{$line[$place{'gene'}]}->[$i] = ($line[$place{'IPscore'}] == $maxINPscore) ? 1 : 0;
+$source_by_gene->{$indirect ? $Pair : $line[$place{'pair'}]}->{$line[$place{'gene'}]}->{$line[$place{'clusterID'}]}->[$i] = ($line[$place{'IPscore'}] == $maxINPscore) ? 1 : 0;
+next;
+}
+if ($i == $place{'pair'}) {
+$source_by_cluster->{$Pair}->{$line[$place{'clusterID'}]}->{$line[$place{'gene'}]}->[$i] = $Pair;
+$source_by_gene->{$Pair}->{$line[$place{'gene'}]}->{$line[$place{'clusterID'}]}->[$i] = $Pair;
+next;
+}}
+$source_by_cluster->{$indirect ? $Pair : $line[$place{'pair'}]}->{$line[$place{'clusterID'}]}->{$line[$place{'gene'}]}->[$i] = $line[$i];
+$source_by_gene->{$indirect ? $Pair :$line[$place{'pair'}]}->{$line[$place{'gene'}]}->{$line[$place{'clusterID'}]}->[$i] = $line[$i];
+}}
+return;
+}
+
+sub findOrthos { #initially picks up orthologs in the first pair of genomes
+my($a, $thepair) = @_;
+my($set, $sm, $i, $newel);
+
+return(undef) if $source_by_taken->{$thepair}->{$a};
+for (keys(%{$source_by_cluster->{$thepair}->{$a}})) {
+$newel = $#{$seeds} + 1;
+for $i(0..($nplaces - 1)) {
+$seeds->[$newel]->[$i] = $source_by_cluster->{$thepair}->{$a}->{$_}->[$i];
+}
+$source_by_taken->{$thepair}->{$a} = 1;
+}
+return $seeds;
+}
+
+sub findNewOrtho { #adds orthologs from the remaining genome pairs
+my($g, $thepair) = @_;
+my($new, $ii, $j, $jj, $sm, $newel);
+
+for (keys(%{$source_by_gene->{$thepair}->{$g}})) {
+next if $source_by_taken->{$thepair}->{$_};
+$newel = $#{$new} + 1;
+for $jj(@{$source_by_gene->{$thepair}->{$g}->{$_}}) {
+$new->[$newel]->[$j] = $jj;
+$j++;
+}
+}
+if (scalar(@{$new}) == 1) {
+$new = findOrthos($new->[0]->[$place{'clusterID'}], $new->[0]->[$place{'pair'}]);
+	if (scalar(@{$new}) > 1) {
+return($new);}
+	else {print  "Unpaired  seed ortholog...$new->[0]->[$place{'gene'}]\n";}
+}
+elsif (scalar(@{$new}) > 1) {
+	print  "Multiple  seed orthologs...\nPair '$thepair'\tGene '$g'";
+}
+return(undef);
+}
+
+sub isNew {
+my($seeds, $new) = @_;
+my($ii);
+
+for $ii(@{$seeds}) {
+if (($ii->[$place{'gene'}] eq $new->[$place{'gene'}]) and ($ii->[$place{'pair'}] eq $new->[$place{'pair'}])) {
+return(undef);
+}
+}
+return(1);
+}
+
+sub pairWiseDist2All { #between-gene distances for algortihm 'ToAllSorted'; deprecated
+my($seeds) = @_;
+my($i, $j, $ii, $jj, $new, $old, $same, $le, $distances, $ke, $va);
+
+$le = scalar(@{$seeds});
+
+for ($i = 0; $i < $le; $i++) {
+$ii = $seeds->[$i]->[$place{'gene'}];
+#next if $distances->{$ii}->{$jj};
+for ($j = 0; $j < $i; $j++) {
+$jj = $seeds->[$j]->[$place{'gene'}];
+undef $same; undef $old; undef $new;
+$same = 1 if ($seeds->[$i]->[$place{'species'}] eq $seeds->[$j]->[$place{'species'}]);
+if ($same) {
+$old = $distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]};}
+else {$old = $distances->{$ii}->{$jj};}
+
+next if ($seeds->[$i]->[$place{'pair'}] ne $seeds->[$j]->[$place{'pair'}]);
+#THEY DESCRIBE THE SAME PAIR OF GENOMES
+if ($same) { 
+#THEY ARE FROM THE SAME SPECIES 
+#next if $distances->    {$ii}->{$jj}->{$seeds->[$i]->[$place{'species'}]};
+	if (!$seeds->[$i]->[$place{'main'}] and !$seeds->[$j]->[$place{'main'}]) { #BOTH ARE IN-PARALOGS
+	$distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]} = $distances->{$jj}->{$ii}->{$seeds->[$i]->[$place{'pair'}]} = $seeds->[$i]->[$place{'IPscore'}] * $seeds->[$j]->[$place{'IPscore'}];
+	}
+	elsif ($seeds->[$i]->[$place{'main'}]) { #THIS ONE IS IN-PARALOG
+	$distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]} = $distances->{$jj}->{$ii}->{$seeds->[$i]->[$place{'pair'}]} = $seeds->[$j]->[$place{'IPscore'}];
+	}
+	elsif ($seeds->[$j]->[$place{'main'}]) { #THIS ONE IS IN-PARALOG
+	$distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]} = $distances->{$jj}->{$ii}->{$seeds->[$i]->[$place{'pair'}]} = $seeds->[$i]->[$place{'IPscore'}];
+	}
+	else { #BOTH ARE SEED ORTHOLOGS
+	$distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]} = $distances->{$jj}->{$ii}->{$seeds->[$i]->[$place{'pair'}]} = $maxINPscore;
+	}
+$new = $distances->{$ii}->{$jj}->{$seeds->[$i]->[$place{'pair'}]};
+}	
+else { 
+#THEY ARE FROM THE DIFFERENT SPECIES
+if ($seeds->[$i]->[$place{'main'}] and $seeds->[$j]->[$place{'main'}]) #BOTH ARE SEED ORTHOLOGS
+{
+	$distances->{$ii}->{$jj} 	= inpDist($seeds, $i, $j);
+	$distances->{$jj}->{$ii} 	= inpDist($seeds, $j, $i);
+}
+elsif ($seeds->[$i]->[$place{'main'}] or $seeds->[$j]->[$place{'main'}]) #STILL, ONE OF THEM IS IN-PARALOG (NO MATTER WHICH)
+{
+	$distances->{$ii}->{$jj}	= 
+	$distances->{$jj}->{$ii} 	= 
+inpDist ($seeds, $i, $j) * inpDist ($seeds, $j, $i)	;
+}
+else 
+#BOTH ARE IN-PARALOGS 
+{
+	$distances->{$ii}->{$jj}	= 
+mainDist($seeds, $i, $j) 	* 
+inpDist ($seeds, $i, $j) 	* 
+inpDist ($seeds, $j, $i)	;
+	$distances->{$jj}->{$ii} 	= 
+mainDist($seeds, $j, $i) 	* 
+inpDist ($seeds, $i, $j) 	* 
+inpDist ($seeds, $j, $i)	;
+}
+}
+$new = $distances->{$ii}->{$jj};
+if (!$same) {print "Distance $ii-$jj is $new\n" if $debug; print "Distance $jj-$ii is $new\n" if $debug;}
+else {
+if ($debug) {
+print "Distance $ii-$jj is\n";
+while (($ke, $va) = each(%{$distances->{$ii}->{$jj}})) {
+print "\tfor $ke: $va\n";
+}
+}
+}
+print "Distance $ii-$jj is not equal to old one $old\n" if ($old and ($old != $new));
+}
+}
+#for ($k = 0; $k < $le; $k++) {$distances->[$k]->[$k] = 1;}
+return($distances);
+}
+
+sub pairWiseDist2Main ($) {#between-gene distances for algortihm 'OnlyMains'
+my($seeds) = @_;
+my($le, $i, $j, $ii, $jj, $new, $old, $distances);
+
+$le = scalar(@{$seeds});
+#$le2 = scalar(@{$species});
+for ($i = 0; $i < $le; $i++) {
+$ii = $seeds->[$i]->[$place{'gene'}];
+for ($j = 0; $j < $i; $j++) {
+$jj = $seeds->[$j]->[$place{'gene'}];
+undef $old; undef $new;
+$old = $distances->{$ii}->{$jj};
+next if ($seeds->[$i]->[$place{'pair'}] ne $seeds->[$j]->[$place{'pair'}]);
+next if	($seeds->[$i]->[$place{'main'}] and $seeds->[$j]->[$place{'main'}]); #SEED ORTHOLOGS WILL BE CLUSTERED ANYWAY 
+if	($seeds->[$i]->[$place{'species'}] eq $seeds->[$j]->[$place{'species'}]) {
+#if (!$use_bootstrap) {$distances->{$ii}->{$jj} = $distances->{$jj}->{$ii} = $maxINPscore ;next;}
+next if !$toMainOrthologOfSelf;
+$distances->{$ii}->{$jj} = $distances->{$jj}->{$ii} = 
+$seeds->[$j]->[$place{'IPscore'}] if $seeds->[$i]->[$place{'main'}];
+$distances->{$ii}->{$jj} = $distances->{$jj}->{$ii} = 
+$seeds->[$i]->[$place{'IPscore'}] if $seeds->[$j]->[$place{'main'}];
+}			#THEY ARE FROM THE SAME SPECIES AND THE DISTANCE IS NOT USED
+else 	{ 	#THEY ARE FROM DIFFERENT SPECIES
+if ($seeds->[$i]->[$place{'main'}] or $seeds->[$j]->[$place{'main'}]) {
+#ONE OF THEM IS SEED ORTHOLOG (NO MATTER WHICH)
+	$distances->{$ii}->{$jj}	= 
+	$distances->{$jj}->{$ii} 	= 
+inpDist ($seeds, $i, $j) 	* 
+inpDist ($seeds, $j, $i)	;
+}
+else {
+#BOTH ARE IN-PARALOGS
+	$distances->{$ii}->{$jj}	= 
+mainDist($seeds, $i, $j) 	* 
+inpDist ($seeds, $i, $j) 	* 
+inpDist ($seeds, $j, $i)	;
+	$distances->{$jj}->{$ii} 	=
+mainDist($seeds, $j, $i) 	* 
+inpDist ($seeds, $i, $j) 	* 
+inpDist ($seeds, $j, $i)	;
+}
+}
+$new = $distances->{$ii}->{$jj};
+print "Distance $ii-$jj is $new\n" if $debug;
+print "Distance $jj-$ii is $new\n" if $debug;
+print "Distance $ii-$jj is not equal to old one $old\n" if ($old and ($old != $new));
+}
+}
+return($distances);
+}
+
+sub mainDist ($$$) { #finds distances between two main (seed) orthologs
+my($seeds, $from, $to) = @_;
+my($ii, $pair1, $pair2, $sum, $nu, $nc);
+
+return($maxINPscore) if !$use_bootstrap; #if we think bootstrap values are not relevant in calculating the distance, then every Main-Main distance should bemaxINPscore = 1 (and this is the default)
+$pair1 = $seeds->[$from]->[$place{'species'}].'-'.$seeds->[$to]->[$place{'species'}];
+$pair2 = $seeds->[$to]->[$place{'species'}].'-'.$seeds->[$from]->[$place{'species'}];
+$sum = $nc = $nu = 0;
+
+for $ii(@{$seeds}) {
+	if (
+	($ii->[$place{'main'}]) and 
+	(($ii->[$place{'pair'}] eq $pair1) or ($ii->[$place{'pair'}] eq $pair2)) and 
+	($ii->[$place{'species'}]) eq $seeds->[$from]->[$place{'species'}]) {
+	$nc++;
+	$sum += $ii->[$place{'IPscore'}];
+	}
+}
+
+if (!$nc) {
+print "Distance $seeds->[$from]->[$place{'gene'}]-$seeds->[$to]->[$place{'gene'}] (pair $pair1 or $pair2) not found\n";
+return(undef);
+}
+else 		
+{
+return($sum / $nc);
+}
+}
+
+sub inpDist ($$$) { #finds a distance from main (seed) ortholog to in-paralog
+my($seeds, $from, $to) = @_;
+my($le, $ii, $pair1, $pair2, $sum, $nu, $nc);
+
+return($maxINPscore) if ($seeds->[$from]->[$place{'main'}] and !$use_bootstrap);
+$le = scalar(@{$seeds});
+$pair1 = $seeds->[$from]->[$place{'species'}].'-'.$seeds->[$to]->[$place{'species'}];
+$pair2 = $seeds->[$to]->[$place{'species'}].'-'.$seeds->[$from]->[$place{'species'}];
+$sum = $nc = $nu = 0;
+for $ii(@{$seeds}) {
+	if (
+	($ii->[$place{'gene'}] eq $seeds->[$from]->[$place{'gene'}]) and 
+	(($ii->[$place{'pair'}] eq $pair1) or 
+	($ii->[$place{'pair'}] eq $pair2))) {
+return($ii->[$place{'IPscore'}]);
+	}
+}
+print "Distance $seeds->[$from]->[$place{'gene'}]-$seeds->[$to]->[$place{'gene'}] not found\n";
+return undef;
+}
+
+sub sortBy ($$) {
+my($num, $ar) = @_;
+my($i, $max, $maxnum, @sorted);
+
+#array2StdOut($ar, 'Before');
+
+LINE001: while (scalar(@{$ar}) > 0) {
+if (scalar(@{$ar}) == 1 and !$ar->[$i]->[$num]) {
+last;
+}
+$max = 0;
+undef $maxnum;
+for ($i = 0; $i < scalar(@{$ar}); $i++) {
+last if !$ar->[$i]->[$num];
+if ($ar->[$i]->[$num] > $max) {
+$max = $ar->[$i]->[$num];
+$maxnum = $i;
+}
+}
+if (defined($maxnum)) {
+push @sorted, splice(@{$ar}, $maxnum, 1);
+next LINE001;
+}
+}
+return(\@sorted);
+}
+
+sub setUnique ($) { #removes duplicated entries from the (pre-)cluster
+my($seeds) = @_;
+my($i, $j, $unique, $sds);
+
+$sds->[$place{'clusterID'}] = $seeds->[$place{'clusterID'}];
+for ($i = 1; $i < scalar(@{$seeds}); $i++) {
+$unique = 1;
+for ($j = 0; $j < scalar(@{$sds}); $j++) {
+if (($seeds->[$i]->[$place{'species'}] eq $sds->[$j]->[$place{'species'}]) and ($seeds->[$i]->[$place{'gene'}] eq $sds->[$j]->[$place{'gene'}]))
+{$unique = 0; 
+last;}
+}
+if ($unique) {push(@{$sds}, $seeds->[$i]);}
+}
+return($sds);
+}
+
+sub isAlready ($$) {
+my($as, $included) = @_;
+my($ai);
+
+for $ai(@{$included}) {
+return(1) if ($ai->[4] eq $as);
+}
+return(undef);
+}
+
+sub alreadyClustered { #helps to avoid clustering same gene twice. Of two alternatives, the one is chosen where the gene is a main (seed) ortholog or was included first. 
+my($g, $cco) = @_;
+my($ai);
+
+return(undef) if !defined($out->{'byName'}->{$g->[$place{'gene'}]}->{$cco});
+
+if ($out->{'byRecord'}->[$out->{'byName'}->{$g->[$place{'gene'}]}->{$cco}]->[3]) {
+return 1;
+}
+else {
+undef $out->{'byRecord'}->[$out->{'byName'}->{$g->[$place{'gene'}]}->{$cco}];
+return(undef);
+}}
+
+sub firstMains { #seed orthologs are included unconditionally
+my($seeds) = @_;
+my($i, $le, @included);
+
+$le = scalar(@{$seeds});
+for ($i = 0; $i < $le; $i++) {
+# and ($seeds->[$i]->[$place{'IPscore'}] == 1)
+if ($seeds->[$i]->[$place{'main'}]) {
+push @included, $seeds->[$i];
+}
+}
+return(@included);
+}
+
+sub getOthers ($$$$) { #retains only genes with distance (well, it is in fact a SIMILARITY) above the cut-off $cco. If it is not set, or equals to 0, the procedure just returns IPscore as a reference - to be saved in the output file.
+my($seeds, $distances, $included, $cco) = @_;
+my($i, $le, $les2, $nc, $ii, $jj, $dist, $ad, $nai, @others);
+
+$le = scalar(@{$seeds});
+for $ii(@{$seeds}) {
+next if isAlready($ii->[$place{'gene'}], $included);
+undef $dist; undef $nc;
+for $jj(@{$included}) {
+next if (($jj->[$place{'species'}] eq $ii->[$place{'species'}]) and !$toMainOrthologOfSelf);
+if (!$distances->{$ii->[$place{'gene'}]}->{$jj->[$place{'gene'}]}) {
+print "The distance between $ii->[$place{'gene'}] and $jj->[$place{'gene'}] does not exist...\n" if $debug; 
+next;
+} 
+if ($jj->[$place{'main'}]) {
+print "( $ii->[$place{'gene'}] - $jj->[$place{'gene'}] ) + " if $debug;
+$dist += $distances->{$ii->[$place{'gene'}]}->{$jj->[$place{'gene'}]};
+$nc++;
+}
+}
+print " / $nc = ".$dist/$nc."\n" if $debug;
+return(undef) if !$nc;
+if ($dist / $nc >= $cco) {
+push @others, $ii;
+$others[$#others]->[$place{'IPscore'}] = $dist / $nc;
+}
+}
+return(\@others);
+}
+
+sub getClosests ($$$$) { #used only in the deprecated 'ToAllSorted' algorithm
+my($seeds, $distances, $included, $cco) = @_;
+my($ni, $ii, $jj, $kk, $dist, $gotnew, $toadd, $nt, $max);
+
+do {
+undef $gotnew;
+for $ii(@{$seeds}) {
+next if isAlready($ii->[$place{'gene'}], $included);
+undef $ni; undef $dist; undef $max;
+for $jj(@{$included}) {
+undef $nt; undef $toadd;
+print "$ii->[$place{'gene'}] vs $jj->[$place{'gene'}] \n" if $debug;
+if ($ii->[$place{'species'}] ne $jj->[$place{'species'}]) {
+$toadd = $distances->{$ii->[$place{'gene'}]}->{$jj->[$place{'gene'}]};
+}
+else {
+for $kk(keys(%{$distances->{$ii->[$place{'gene'}]}->{$jj->[$place{'gene'}]}})) {
+$toadd += $distances->{$ii->[$place{'gene'}]}->{$jj->[$place{'gene'}]}->{$kk}; $nt++;
+}
+$toadd = $toadd / $nt if $nt;
+}
+$dist += $toadd; $ni++ if $toadd;
+print "A distance for $ii->[$place{'gene'}] and $jj->[$place{'gene'}] does not exist...\n" if (!$toadd and $debug);
+}
+if ($ni and ($dist / $ni > $max->['IPscore'])) {
+$max = $ii; $max->['IPscore'] = $dist / $ni;
+}
+if ($max->['IPscore'] >= $cco) {
+print "Included $max->[4] as $dist / $ni > $cco\n" if $debug;
+push(@{$included}, $max);
+$gotnew = 1;
+}
+}
+} while ($gotnew);
+return($included);
+}
+
+sub array2StdOut { #for debug purpose only
+my($ar, $name) = @_;
+my($ii, $jj);
+
+print "$name: \n";
+return(0) if !scalar(@{$ar});
+for $ii(@{$ar}) {
+for $jj(@{$ii}) {
+print "$jj\t" if defined($jj);
+}
+print "\n";
+}
+return undef;
+}