Search results for "distribution:BioPerl-Run Bio::DB::Taxonomy::list"
Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*
This module allows the user to query the NCBI Entrez database via its SOAP (Simple Object Access Protocol) web service (described at <http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.h tml>). The basic tools ("einfo, esearch, eli...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy
This is a wrapper for running the Semphy application by N. Friedman et a.. You can get details here: http://compbio.cs.huji.ac.il/semphy/. Semphy is used for phylogenetic reconstruction (making a tree with branch lengths from an aligned set of input ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::DB::SoapEUtilities::FetchAdaptor::species - Fetch adaptor for 'taxonomy' efetch SOAP messages
Returns an iterator over Bio::Species objects: my $fac = Bio::DB::SoapEUtilities->new; my $taxio = $fac->efetch(-db => 'taxonomy', -id => 1394)->run(-auto_adapt=>1); my $sp = $taxio->next_species; $sp->binomial; # returns 'Bacillus caldolyticus' To f...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::DB::SoapEUtilities::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects
"FetchAdaptor" is the base class of a system, modeled after Bio::SeqIO, to parse SOAP responses from the NCBI Entrez "efetch" utility into germane BioPerl objects. The user will rarely need to instantiate a "FetchAdaptor" with Bio::DB::SoapEUtilities...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::DB::SoapEUtilities::DocSumAdaptor - Handle for Entrez SOAP DocSums
This adaptor provides an iterator ("next_docsum()") and other convenience functions for parsing NCBI Entrez EUtility "esummary" SOAP results....
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit
This is a wrapper for running the phyloFit application by Adam Siepel. You can get details here: http://compgen.bscb.cornell.edu/~acs/software.html Currently the interface is extremely simplified. Only the --tree form of usage is allowed (not --init-...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Phast::PhastCons - Wrapper for footprinting using phastCons
This is a wrapper for running the phastCons application by Adam Siepel. You can get details here: http://compgen.bscb.cornell.edu/~acs/software.html phastCons is used for phylogenetic footprinting/ shadowing. Currently the interface is extremely simp...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC