/usr/share/perl5/Bio/Tools/Run/Phylo/ 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/Phylo/FastTree.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Gumby.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/
/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/
/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/
/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/
/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/PhyloBase.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm
/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm