Search results for "Bio::Tools::Run::Analysis"
Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis tool
The module represents an access to the local and/or remote analysis tools in a unified way that allows adding new access methods (protocols) seamlessly. At the moment of writing, there is available a *SOAP* access to almost all EMBOSS applications, r...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Tools::Run::AnalysisFactory - A directory of analysis tools
- Bio::AnalysisI - An interface to any (local or remote) analysis tool
- Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
- 6 more results from BioPerl »
Bio::Tools::Run::Analysis::soap - A SOAP-based access to the analysis tools
This object allows to execute and to control a remote analysis tool (an application, a program) using the SOAP middleware, All its public methods are documented in the interface module "Bio::AnalysisI" and explained in tutorial available in the "anal...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools
- Bio::Tools::Run::Coil - wrapper for ncoils program
- Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program
- 15 more results from BioPerl-Run »
Tutorial - Hands-on tutorial for using Bio::NEXUS module.
Tutorial to get started using Bio::NEXUS module. INTRODUCTION The NEXUS file format standard of Maddison, et al. (1997) is designed to represent sets of data, including character data (e.g., molecular sequence alignments, morphological character sets...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution
bioseq - Manipulation of FASTA sequences based on BioPerl
bioseq is a command-line utility for common, routine sequence manipulations based on BioPerl modules including Bio::Seq, Bio::SeqIO, Bio::SeqUtils, and Bio::Tools::SeqStats. By default, bioseq assumes that both the input and the output files are in F...
YZHERNAND/Bio-BPWrapper-1.15 - 27 Feb 2024 16:55:31 UTC - Search in distribution
Bio::ViennaNGS - A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Bio::ViennaNGS is a distribution of Perl modules and utilities for building efficient Next-Generation Sequencing (NGS) analysis pipelines. It covers various aspects of NGS data analysis, including (but not limited to) conversion of sequence annotatio...
MTW/Bio-ViennaNGS-v0.19.2 - 11 Dec 2018 13:25:00 UTC - Search in distribution
cipresrun - command line interface to the CIPRES analysis portal
RVOSA/Bio-Phylo-CIPRES-v0.2.1
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17 Apr 2020 22:55:30 UTC
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- Bio::Phylo::CIPRES - Reusable components for CIPRES REST API access
FortyTwo::Manual - User Guide for Forty-Two
DBAURAIN/Bio-MUST-Apps-FortyTwo-0.213470
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13 Dec 2021 23:13:33 UTC
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cx-genbank2chaos.pl.pl
Converts a genbank file to a chaos xml file (or a collection of chaos xml files). The genbank file is 'unflattened' in order to infer the relationships between features with the -islands option set, this loops through a list of genbank-formatted file...
CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution
Bio::Homology::InterologWalk - Retrieve, prioritise and visualize putative Protein-Protein Interactions through interolog mapping
A common activity in computational biology is to mine protein-protein interactions from publicly available databases to build *Protein-Protein Interaction* (PPI) datasets. In many instances, however, the number of experimentally obtained annotated PP...
GGALLONE/Bio-Homology-InterologWalk-0.58 - 01 Feb 2012 12:31:34 UTC - Search in distribution
Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
This module is used to parse the output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the PAML programs, but this module is only useful to parse t...
CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 UTC - Search in distribution- Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml
- Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML
- Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml
- 3 more results from Bio-Tools-Phylo-PAML »
Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Note: this DESCRIPTION only documents the Bioperl interface to Clustalw. Clustalw, itself, is a large & complex program - for more information regarding clustalw, please see the clustalw documentation which accompanies the clustalw distribution. Clus...
CDRAUG/Bio-Tools-Run-Alignment-Clustalw-1.7.4 - 11 Jul 2018 14:57:04 UTC - Search in distribution
Bio::Tools::Run::QCons - Run Qcons to analyze protein-protein contacts
This module implements a wrapper for the QCons application. QCons itself is an implementation of the Polyhedra algorithm for the prediction of protein-protein contacts. From the program's web page (<http://tsailab.tamu.edu/QCons/>): "QContacts allows...
BRUNOV/Bio-Tools-Run-Qcons-0.112881 - 15 Oct 2011 21:39:17 UTC - Search in distribution
Alien::SeqAlignment::hmmer3 - find, build and install the hmmer3 tools
This distribution provides HMMER3 so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the HMMER3 website, if the HMMER3 is not found in the system path. The url used is : http://eddylab.org/sof...
CHRISARG/Alien-SeqAlignment-hmmer3-0.03 - 24 Mar 2024 03:13:58 UTC - Search in distribution