/usr/share/perl5/Bio/Tools/Run/Alignment/ is in libbio-perl-run-perl 1.7.1-3.
This file is owned by root:root, with mode 0o755.
..
/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Clustalw.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm
/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm