updated manual-est with description of pangenome matrix versions taken from tutorial

Author: eead-csic-compbio

CHANGES.txt

@@ -398,3 +398,4 @@
 15062022: added sub same_sequence_order to lib/phyTools.pm
 15062022: get_homologues-est.pl now checks that CDS .fna & .faa sequences are in same order (thanks V Guignon!)
 22082022: when checking that .fna & .faa sequences are in same order, CDSs with Ns are skipped (B Chapman) 
+22082022: updated manual-est with description of pangenome matrix versions taken from tutorial

lib/phyTools.pm

@@ -595,7 +595,7 @@ sub same_sequence_order
     $translated =~ s/\*$//g;
     $parsed =~ s/\*$//g;
 
-    if($parsed ne $translated &&
+    if($parsed ne $translated && 
       $parsed !~ /$translated/ && $translated !~ /$parsed/) {
       print "# same_sequence_order : sequence #$seq does not match: ".
           "$refCDSnt->[$seq][SEQ]\n$translated\n$refCDSaa->[$seq][SEQ]\n";