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<div style="font-family:Helvetica,Arial;font-size:13px; ">Hi Carson,</div>
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<div style="font-family:Helvetica,Arial;font-size:13px; ">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. </div>
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<div style="font-family:Helvetica,Arial;font-size:13px; ">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)</div>
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<div style="font-family:Helvetica,Arial;font-size:13px; ">Thanks</div>
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<div style="font-family:Helvetica,Arial;font-size:13px; ">chris</div>
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<div style="margin: 0px;">Bio::DB::Fasta</div>
<div style="margin: 0px;">Bio::DB::GFF</div>
<div style="margin: 0px;">Bio::FeatureIO::gff</div>
<div style="margin: 0px;">Bio::Search::HSP::GenericHSP</div>
<div style="margin: 0px;">Bio::Search::HSP::HSPFactory</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::Base</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::augustus</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::blastn</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::blastx</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::cdna2genome</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::est2genome</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::fgenesh</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::genemark</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::gff3</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::protein2genome</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::repeatmasker</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::snap</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::snoscan</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::tblastx</div>
<div style="margin: 0px;">Bio::Search::HSP::PhatHSP::trnascan</div>
<div style="margin: 0px;">Bio::Search::Hit::GenericHit</div>
<div style="margin: 0px;">Bio::Search::Hit::HitFactory</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::Base</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::augustus</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::blastn</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::blastx</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::cdna2genome</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::est2genome</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::fgenesh</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::genemark</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::gff3</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::protein2genome</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::repeatmasker</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::snap</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::snoscan</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::tblastx</div>
<div style="margin: 0px;">Bio::Search::Hit::PhatHit::trnascan</div>
<div style="margin: 0px;">Bio::Search::Result::ResultFactory</div>
<div style="margin: 0px;">Bio::SearchIO</div>
<div style="margin: 0px;">Bio::SeqIO</div>
<div style="margin: 0px;">Bio::Tools::CodonTable</div>
<div style="margin: 0px;">Bio::Tools::GFF</div>
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