Search results for "dist:BioPerl-Run Bio::Tree::Tree"
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::Phylo::QuickTree - Wrapper for rapid reconstruction of phylogenies using QuickTree
This is a wrapper for running the QuickTree application by Kevin Howe. You can download it here: http://www.sanger.ac.uk/Software/analysis/quicktree/ Currently only input with alignments and output of trees is supported. (Ie. no support for distance ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees
This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite. To set parameters with option you need to pass in an array reference or a string, depending on the parameter. For example: $treedraw->HORIZMARGINS(['2.00','2.5']...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
This script requires that the bioperl-run pkg be also installed....
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
This is a wrapper around the Simprot program by Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier. Simprot allows for several models of amino acid substitution (PAM, JTT and PMB), allows for gamma distributed sites rates according to ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::LVB - Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1.
Wrapper for LVB, which uses a simulated annealing heuristic search to seek parsimonious trees from a nucleotide multiple alignment....
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::Phylip::ProtPars - Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
CJFIELDS/BioPerl-Run-1.007003
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08 Feb 2019 19:55:33 UTC
Bio::Tools::Run::Phylo::Gerp - Wrapper for GERP
This is a wrapper for running the GERP (v2) programs 'gerpcol' and 'gerpelem' by Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here: http://mendel.stanford.edu/sidowlab/. GERP can be used for phylogenetic footprinting/ sha...
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::Tools::Run::FootPrinter - wrapper for the FootPrinter program
From the FootPrinter manual: FootPrinter is a program that performs phylogenetic footprinting. It takes as input a set of unaligned orthologous sequences from various species, together with a phylogenetic tree relating these species. It then searches...
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::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::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results
This module attempts to make Entrez Utilities SOAP responses as user-friendly and intuitive as possible. These responses can be complex structures with much useful data; but users will generally desire the values of some key fields. The Result object...
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::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
To run mlagan/lagan, you must have an environment variable that points to the executable directory with files lagan.pl etc. "LAGAN_DIR=/opt/lagan_executables/" Simply having the executables in your path is not supported because the executables themse...
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::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::Phylo::Hyphy::Base - Hyphy wrapping base methods
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