BioPerl and MAKER

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BioPerl and MAKER

Fields, Christopher J
Hi Carson,

I’ll be working over the next several months to push out a new stripped-down version of BioPerl (along with the help of Carne Draug) with the hopeful target goal of a CPAN release in April-May.  I know MAKER still relies on a few BioPerl core modules, such as those related to codon tables, FASTA indexing, etc.   

Just from a quick grep through the latest release (2.31.10) I found the ones at the bottom of the email; I know the various Phat* modules are MAKER-specific, but can you think of any others that might be required?  (I haven’t checked the 3.0 beta version yet)

Thanks

chris

Bio::DB::Fasta
Bio::DB::GFF
Bio::FeatureIO::gff
Bio::Search::HSP::GenericHSP
Bio::Search::HSP::HSPFactory
Bio::Search::HSP::PhatHSP::Base
Bio::Search::HSP::PhatHSP::augustus
Bio::Search::HSP::PhatHSP::blastn
Bio::Search::HSP::PhatHSP::blastx
Bio::Search::HSP::PhatHSP::cdna2genome
Bio::Search::HSP::PhatHSP::est2genome
Bio::Search::HSP::PhatHSP::fgenesh
Bio::Search::HSP::PhatHSP::genemark
Bio::Search::HSP::PhatHSP::gff3
Bio::Search::HSP::PhatHSP::protein2genome
Bio::Search::HSP::PhatHSP::repeatmasker
Bio::Search::HSP::PhatHSP::snap
Bio::Search::HSP::PhatHSP::snoscan
Bio::Search::HSP::PhatHSP::tblastx
Bio::Search::HSP::PhatHSP::trnascan
Bio::Search::Hit::GenericHit
Bio::Search::Hit::HitFactory
Bio::Search::Hit::PhatHit::Base
Bio::Search::Hit::PhatHit::augustus
Bio::Search::Hit::PhatHit::blastn
Bio::Search::Hit::PhatHit::blastx
Bio::Search::Hit::PhatHit::cdna2genome
Bio::Search::Hit::PhatHit::est2genome
Bio::Search::Hit::PhatHit::fgenesh
Bio::Search::Hit::PhatHit::genemark
Bio::Search::Hit::PhatHit::gff3
Bio::Search::Hit::PhatHit::protein2genome
Bio::Search::Hit::PhatHit::repeatmasker
Bio::Search::Hit::PhatHit::snap
Bio::Search::Hit::PhatHit::snoscan
Bio::Search::Hit::PhatHit::tblastx
Bio::Search::Hit::PhatHit::trnascan
Bio::Search::Result::ResultFactory
Bio::SearchIO
Bio::SeqIO
Bio::Tools::CodonTable
Bio::Tools::GFF


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