Kwalitee Issues


Change the permissions of Build.PL/Makefile.PL to not-executable.


Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.


Add =head1 LICENSE and the text of the license to the main module in your code.


Run a proper command ("make manifest" or "./Build manifest", maybe with a force option), or use a distribution builder to generate the MANIFEST. Or update MANIFEST manually.


  • MANIFEST (224) does not match dist (225):
  • Missing in MANIFEST: doc/._changes.txt


Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: Bio-NEXUS-0.78/exec/ -- Around line 68: Unknown directive: =ignore


Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.


Add a META.json to the distribution. Your buildtool should be able to autogenerate it.


If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.


Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.


If you use Mac OS X, set COPYFILE_DISABLE (for OS 10.5 and better) or COPY_EXTENDED_ATTRIBUTES_DISABLE (for OS 10.4) environmental variable to true to exclude dot underscore files from a distribution.


  • doc/._changes.txt


Fix the version numbers so that version::is_lax($version) returns true.


  • lib/Bio/NEXUS/ HASH(0x70329e0)
  • lib/Bio/NEXUS/ HASH(0x704e580)
  • lib/Bio/NEXUS/ HASH(0x704e568)
  • lib/Bio/NEXUS/ HASH(0x70247f0)
  • lib/Bio/NEXUS/ HASH(0x70328d8)
  • lib/Bio/NEXUS/ HASH(0x70291d0)
  • lib/Bio/NEXUS/ HASH(0x7032980)
  • lib/Bio/NEXUS/ HASH(0x70246a0)
  • lib/Bio/NEXUS/ HASH(0x7039940)
  • lib/Bio/NEXUS/ HASH(0x7068010)
  • lib/Bio/NEXUS/ HASH(0x70bfd58)
  • lib/Bio/NEXUS/ HASH(0x703c950)
  • lib/Bio/NEXUS/ HASH(0x7032800)
  • lib/Bio/NEXUS/ HASH(0x703a3f0)
  • lib/Bio/NEXUS/ HASH(0x70374c8)
  • lib/Bio/NEXUS/ HASH(0x70373f0)
  • lib/Bio/NEXUS/ HASH(0x7024f58)
  • lib/Bio/NEXUS/Tools/ HASH(0x7021eb0)
  • lib/Bio/NEXUS/Tools/ HASH(0x7000d10)
  • lib/Bio/NEXUS/Tools/ HASH(0x7024e68)
  • lib/Bio/NEXUS/ HASH(0x7039a60)
  • lib/Bio/NEXUS/ HASH(0x7024e20)
  • lib/Bio/NEXUS/ HASH(0x7024d60)
  • lib/Bio/NEXUS/ HASH(0x702bb50)
  • lib/Bio/NEXUS/ HASH(0x702c390)


Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::NEXUS, Bio::NEXUS::AssumptionsBlock, Bio::NEXUS::Block, Bio::NEXUS::CharactersBlock, Bio::NEXUS::CodonsBlock, Bio::NEXUS::DataBlock, Bio::NEXUS::DistancesBlock, Bio::NEXUS::Functions, Bio::NEXUS::HistoryBlock, Bio::NEXUS::Matrix, Bio::NEXUS::NHXCmd, Bio::NEXUS::Node, Bio::NEXUS::NotesBlock, Bio::NEXUS::SetsBlock, Bio::NEXUS::SpanBlock, Bio::NEXUS::TaxUnit, Bio::NEXUS::TaxUnitSet, Bio::NEXUS::TaxaBlock, Bio::NEXUS::Tools::GraphicsParams, Bio::NEXUS::Tools::NexModifier, Bio::NEXUS::Tools::NexPlotter, Bio::NEXUS::Tree, Bio::NEXUS::TreesBlock, Bio::NEXUS::UnalignedBlock, Bio::NEXUS::UnknownBlock, Bio::NEXUS::Util::Exceptions, Bio::NEXUS::Util::Logger, Bio::NEXUS::WeightSet


Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.


Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).


Name Abstract Version View
Bio::NEXUS An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format 0.78 metacpan
Bio::NEXUS::AssumptionsBlock Represents ASSUMPTIONS block of a NEXUS file metacpan
Bio::NEXUS::Block Provides useful functions for blocks in NEXUS file (parent class). metacpan
Bio::NEXUS::CharactersBlock Represents a CHARACTERS Block (Data or Characters) of a NEXUS file metacpan
Bio::NEXUS::CodonsBlock Represents CODONS block in NEXUS file metacpan
Bio::NEXUS::DataBlock Represents the deprecated DATA Block in NEXUS file. metacpan
Bio::NEXUS::DistancesBlock Represents DISTANCES block in NEXUS file metacpan
Bio::NEXUS::Functions Provides private utiliy functions for the module metacpan
Bio::NEXUS::HistoryBlock Represents a HISTORY block of a NEXUS file metacpan
Bio::NEXUS::Matrix Provides functions for handling blocks that have matrices metacpan
Bio::NEXUS::NHXCmd Provides functions for manipulating nodes in trees metacpan
Bio::NEXUS::Node Provides functions for manipulating nodes in trees metacpan
Bio::NEXUS::NotesBlock Represents a NOTES block in a NEXUS file. metacpan
Bio::NEXUS::SetsBlock Represents SETS block of a NEXUS file metacpan
Bio::NEXUS::SpanBlock Represent SPAN block in a NEXUS file (contains meta data). metacpan
Bio::NEXUS::TaxUnit Represents a taxon unit in a NEXUS file metacpan
Bio::NEXUS::TaxUnitSet Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file metacpan
Bio::NEXUS::TaxaBlock Represents TAXA block of a NEXUS file metacpan
Bio::NEXUS::Tools::GraphicsParams metacpan
Bio::NEXUS::Tools::NexModifier metacpan
Bio::NEXUS::Tools::NexPlotter metacpan
Bio::NEXUS::Tree Provides functions for manipulating trees metacpan
Bio::NEXUS::TreesBlock Represents TREES block of a NEXUS file metacpan
Bio::NEXUS::UnalignedBlock Represents an UNALIGNED block of a NEXUS file metacpan
Bio::NEXUS::UnknownBlock Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module. metacpan
Bio::NEXUS::Util::Exceptions Exception classes for Bio::NEXUS. metacpan
Bio::NEXUS::Util::Logger Logging for Bio::NEXUS. metacpan
Bio::NEXUS::WeightSet Represents column weights in alignment ( for each character) metacpan


Name File View
Bio::NEXUS::Util::StackTrace lib/Bio/NEXUS/Util/ metacpan
MyData lib/Bio/NEXUS/Tools/ metacpan

Other Files

Build.PL metacpan
MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README_admin metacpan