Search results for "dist:BioPerl-Run Bio::AlignIO"
Bio::Factory::EMBOSS - EMBOSS application factory class
The EMBOSS factory class encapsulates access to EMBOSS programs. A factory object allows creation of only known applications. If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The val...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/ You can pass most options understood by the command-line p...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Vista - Wrapper for Vista
Pls see Vista documentation for plotfile options Wrapper for Vista : C. Mayor, M. Brudno, J. R. Schwartz, A. Poliakov, E. M. Rubin, K. A. Frazer, L. S. Pachter, I. Dubchak. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinf...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore
Wrapper module for Sean Eddy's Infernal suite of programs. The current implementation runs cmsearch, cmcalibrate, cmalign, cmemit, cmbuild, cmscore, and cmstat. cmsearch will return a Bio::SearchIO, cmemit a Bio::SeqIO/AlignIO, and cmalign a Bio::Ali...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::RNAMotif - Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune
Wrapper module for Tom Macke and David Cases's RNAMotif suite of programs. This allows running of rnamotif, rmprune, rm2ct, and rmfmt. Binaries are available at http://www.scripps.edu/mb/case/casegr-sh-3.5.html. This wrapper allows for one to save ou...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
The EMBOSSacd represents all the possible command line arguments that can be given to an EMBOSS application. Do not create this object directly. It will be created and attached to its corresponding Bio::Tools::Run::EMBOSSApplication if you set $appli...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program
This is a wrapper around the SLR program. See http://www.ebi.ac.uk/goldman/SLR/ for more information. This module is more about generating the proper ctl file and will run the program in a separate temporary directory to avoid creating temp files all...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Raxml
Get a Bio::Tree object using raxml given a protein or DNA alignment....
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Phyml - Wrapper for rapid reconstruction of phylogenies using Phyml
This is a wrapper for running the phyml application by Stephane Guindon and Olivier Gascuel. You can download it from: http://atgc.lirmm.fr/phyml/ Installing After downloading, you need to rename a the copy of the program that runs under your operati...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::FastTree
Get a Bio::Tree object given a protein or DNA alignment....
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
This DESCRIPTION only documents Bio::Tools::Run::StandAloneBlast, a Bioperl object for running the NCBI standAlone BLAST package. Blast itself is a large & complex program - for more information regarding BLAST, please see the BLAST documentation whi...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Hyphy::REL - Wrapper around the Hyphy REL analysis
This is a wrapper around the REL analysis of HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information. This module will generate ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Hyphy::FEL - Wrapper around the Hyphy FEL analysis
This is a wrapper around the FEL analysis of HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information. This module will generate ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications
The EMBOSSApplication class can represent any EMBOSS program. It is created by a Bio::Factory::EMBOSS object. If you want to check command line options before sending them to the program set $prog->verbose to positive integer. The ADC description of ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Hyphy::SLAC - Wrapper around the Hyphy SLAC analysis
This is a wrapper around the SLAC analysis of HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information....
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Alignment::Pal2Nal - Wrapper for Pal2Nal
This is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You can get details here: http://coot.embl.de/pal2nal/. Pal2Nal is used for aligning a set of nucleotide sequences based on an alignment of their translations. You can try supply...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Njtree::Best - Wrapper around the Njtree (Njtree/phyml) best program.
This is a wrapper around the best program of Njtree by Li Heng. See http://treesoft.sourceforge.net/njtree.shtml for more information. Wrapper for the calculation of a reconciled phylogenetic tree with inferred duplication tags from amultiple sequenc...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*
NOTE: This module requires BLAST+ v. 2.2.24+ and higher. Until the API stabilizes for BLAST+, consider this module highly experimental. This module along with Bio::Tools::Run::StandAloneBlastPlus::BlastMethods allows the user to perform BLAST functio...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML
This is a wrapper for the exe from the Molphy (MOLecular PHYlogenetics) package by Jun Adachi & Masami Hasegawa. The software can be downloaded from <http://www.ism.ac.jp/ismlib/softother.e.html>. Note that PHYLIP (Joe Felsenstein) also provides a ve...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Hyphy::Modeltest - Wrapper around the Hyphy Modeltest analysis
This is a wrapper around the Modeltest analysis of HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org for more information. This module will gen...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC