Tag: BioPerl

Bioinformatics Market Is Set To Reach USD 28.6 Billion By 2030 With CAGR Of 13.73% | Marketdigits

(MENAFN– GlobeNewsWire – Nasdaq) The Global Bioinformatics Market was valued USD 10.23 Billion in 2023 and projected to reach USD 28.6 Billion by 2030, growing at a CAGR of 13.73% during the forecast period of 2023-2030 Richmond, Feb. 09, 2024 (GLOBE NEWSWIRE) — According to a research report ” Bioinformatics…

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Bioinformatics Market is Set to Reach USD 28.6 Billion by

Richmond, Feb. 09, 2024 (GLOBE NEWSWIRE) — According to a research report “Bioinformatics Market”, by tools Type (BLAST, BioPerl, InterMine, Others), Services (Genome Sequencing, RNA sequencing, Metagenomic Analysis, Epigenomic, Others), Application (Drug discovery, Personalized medicine, Preventive medicine, Transcriptions, Metabolomics, Gene therapy, Others) Sectors (Medical Biotechnology, Animal Biotechnology, Plant Biotechnology, Environmental…

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Ubuntu Manpage: Bio::Coordinate – Modules for working with biological coordinates

Provided by: libbio-coordinate-perl_1.7.1-4_all NAME Bio::Coordinate – Modules for working with biological coordinates VERSION version 1.007001 SYNOPSIS # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow $pair1; $pair2; # add them into a Collection $collection = Bio::Coordinate::Collection->new; $collection->add_mapper($pair1); $collection->add_mapper($pair2); # create a position and map it $pos = Bio::Location::Simple->new (-start => 5, -end…

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Ubuntu Manpage: Bio::EUtilities – BioPerl low-level API for retrieving and storing data from NCBI eUtils

Provided by: libbio-eutilities-perl_1.77-2_all NAME Bio::EUtilities – BioPerl low-level API for retrieving and storing data from NCBI eUtils VERSION version 1.77 SYNOPSIS See Bio::DB::EUtilities for example usage with NCBI. DESCRIPTION This distribution encompasses a low-level API for interacting with (and storing) information from) NCBI’s eUtils interface. See Bio::DB::EUtilities for the query…

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man Bio::SeqIO::pir (3): PIR sequence input/output stream

Bio::SeqIO::pir(3) PIR sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION This object can transform Bio::Seq objects to and from pir flat file databases. Note: This does not completely preserve the PIR format – quality information about sequence is currently discarded since…

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Bioinformatics Trainer Part Time Job Opening at Biotecnika

Bioinformatics Trainer Part Time Job Opening at Biotecnika Bangalore Biotecnika Info Labs Pvt Ltd is a leading Bio-IT Company with a diversified portfolio in Information technology and biotechnology. We seek a highly motivated and experienced individual to join our team as a Part-Time Bioinformatics Trainer & Researcher. The successful candidate…

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SSR molecular marker developments and genetic diversity analysis of Zanthoxylum nitidum (Roxb.) DC

Commission, S. P. Pharmacopoeia of the People’s Republic of China (Pharmacopoeia of the People’s Republic of China, 2020). Google Scholar  Sun, X. & Sun, F. Shennong Materia Medica Classic (People’s Health Publishing House, 1963). Google Scholar  Huang, C. Flora of China Vol. 43 (Science Press, 1997). Google Scholar  Hu, J….

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Ubuntu Manpage: Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups

Provided by: libbio-perl-perl_1.7.7-1_all NAME Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups by name. SYNOPSIS my $registry = Bio::Ontology::DocumentRegistry->get_instance(); my($ont,$def,$fmt) = $registry->documents(‘Sequence Ontology’); my $io = Bio::OntologyIO->new(-url => $ont, -defs_url => $def, -format => $fmt); my $so = $io->next_ontology(); #… DESCRIPTION Do not use this directly, use…

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How to install or uninstall “python3-biopython-sql” on Kali Linux ?

1. Install python3-biopython-sql package Please follow the steps below to install python3-biopython-sql package: sudo apt install python3-biopython-sql Copy 2. Uninstall / Remove python3-biopython-sql package Please follow the steps below to uninstall python3-biopython-sql package: sudo apt remove python3-biopython-sql Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of python3-biopython-sql…

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LocationI.pm | searchcode

PageRenderTime 18ms CodeModel.GetById 8ms RepoModel.GetById 0ms app.codeStats 0ms /Bio/LocationI.pm github.com/gjuggler/bioperl-live Perl | 435 lines | 291 code | 126 blank | 18 comment | 23 complexity | d714bd170931ca330fd7baf26e25b1c9 MD5 | raw file # # BioPerl module for…

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Ubuntu Manpage: Bio::MolEvol::CodonModel – Codon Evolution Models

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::MolEvol::CodonModel – Codon Evolution Models SYNOPSIS use Bio::MolEvol::CodonModel; my $codon_path = Bio::MolEvol::CodonModel->codon_path; my ($ns, $syn) = $codon_path->{‘AATAAC’}; print “AAT -> AAC: $ns ns mutations, $syn syn mutations\n”; DESCRIPTION This object is intended to group Codon Evolution Models. Currently it has one method codon_path that returns a…

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Ubuntu Manpage: Bio::Installer::Generic – DESCRIPTION of Object

Provided by: libbio-perl-run-perl_1.6.9-3_all NAME Bio::Installer::Generic – DESCRIPTION of Object SYNOPSIS Give standard usage here DESCRIPTION Describe the object here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation…

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Index of /ubuntu/ubuntu/pool/universe/b/bioperl-run

Name Last modified Size Parent Directory   – bioperl-run_1.6.9-2.debian.tar.gz 2013-11-15 18:13 9.1K bioperl-run_1.6.9-2.dsc 2013-11-15 18:13 1.6K bioperl-run_1.6.9-2_all.deb 2013-11-15 18:33 41K bioperl-run_1.6.9-3.debian.tar.xz 2015-07-03 13:23 8.7K bioperl-run_1.6.9-3.dsc 2015-07-03 13:23 2.2K bioperl-run_1.6.9-3_all.deb 2015-07-03 13:43 39K bioperl-run_1.6.9.orig.tar.gz 2011-06-19 07:04 14M bioperl-run_1.7.1-3.debian.tar.xz 2017-01-13 18:13 12K bioperl-run_1.7.1-3.dsc 2017-01-13 18:13 2.5K bioperl-run_1.7.1-3_all.deb 2017-01-13 18:48 39K bioperl-run_1.7.1.orig.tar.gz 2016-12-22…

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Debian — Details of package bioperl in trixie

Perl tools for computational molecular biology The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. The recommended packages…

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How to Install bioperl-run software package in Ubuntu 16.04 LTS (Xenial Xerus)

How to Install bioperl-run software package in Ubuntu 16.04 LTS (Xenial Xerus) bioperl-run software package provides BioPerl wrappers: scripts, you can install in your Ubuntu 16.04 LTS (Xenial Xerus) by running the commands given below on the terminal, $ sudo apt-get update $ sudo apt-get install bioperl-run bioperl-run is installed…

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How to Install bioperl software package in Ubuntu 16.04 LTS (Xenial Xerus)

How to Install bioperl software package in Ubuntu 16.04 LTS (Xenial Xerus) bioperl software package provides Perl tools for computational molecular biology, you can install in your Ubuntu 16.04 LTS (Xenial Xerus) by running the commands given below on the terminal, $ sudo apt-get update $ sudo apt-get install bioperl…

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Ubuntu Manpage: Bio::Map::MappableI – An object that can be placed in a map

Provided by: libbio-perl-perl_1.7.2-3_all NAME Bio::Map::MappableI – An object that can be placed in a map SYNOPSIS # do not use this module directly # See Bio::Map::Mappable for an example of # implementation. DESCRIPTION This object handles the generic notion of an element placed on a (linear) Map. A Mappable can…

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Linux Certif – Man bp_seqconvert.1p(1) – 2008-06-24 (ubuntu

Rechercher une page de manuel Langue: en Version: 2008-06-24 (ubuntu – 07/07/09) Section: 1 (Commandes utilisateur) NAME seqconvert – generic BioPerl sequence format converter SYNOPSIS seqconvert –from in-format –to out-format < file.in-format > file.out-format # or seqconvert -f in-format -t out-format < file.in-format > file.out-format DESCRIPTION This script gives command…

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Ubuntu Manpage: Bio::Tools::Genewise – Results of one Genewise run

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::Tools::Genewise – Results of one Genewise run SYNOPSIS use Bio::Tools::Genewise; my $gw = Bio::Tools::Genewise(-file=>”genewise.out”); while (my $gene = $gw->next_prediction){ my @transcripts = $gene->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start.” “.$e->end.”\n”; } } } DESCRIPTION This is the parser for the…

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Ubuntu Manpage: Bio::Align::PairwiseStatistics – Base statistic object for Pairwise Alignments

Provided by: libbio-perl-perl_1.7.8-1_all NAME Bio::Align::PairwiseStatistics – Base statistic object for Pairwise Alignments SYNOPSIS use strict; my $stats = Bio::Align::PairwiseStatistics->new(); # get alignment object of two sequences somehow my $pwaln; print $stats->number_of_comparable_bases($pwaln); my $score = $stats->score_nuc($pwaln); DESCRIPTION Calculate pairwise statistics. FEEDBACK Mailing Lists User feedback is an integral part of the…

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Ubuntu Manpage: Bio::Structure::IO::pdb – PDB input/output stream

Provided by: libbio-perl-perl_1.6.923-1_all NAME Bio::Structure::IO::pdb – PDB input/output stream SYNOPSIS It is probably best not to use this object directly, but rather go through the Bio::Structure::IO handler system. Go: $stream = Bio::Structure::IO->new(-file => $filename, -format => ‘PDB’); while (my $structure = $stream->next_structure) { # do something with $structure } DESCRIPTION…

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Contig order rearranged agat

Contig order rearranged agat 0 Hi, I annotated a genome with prokka and while converting to GTF with agat, I get the following error: => Version of the Bioperl GFF parser selected by AGAT: 3 gff3 reader error level1: No ID attribute found @ for the feature: … 1 warning…

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Ubuntu Manpage: bp_seqret – bioperl implementation of sequence fetch from local db (like EMBOSS seqret)

Provided by: bioperl_1.7.7-1_all NAME bp_seqret – bioperl implementation of sequence fetch from local db (like EMBOSS seqret) USAGE bp_seqret [-f/–format outputformat] [-o/–out/–outfile outfile] [-d/–db dbname] [-i/–id/-s/–seqname seqname1] Example usage: bp_seqret -f fasta -db db.fa -i seq1 -i seq2 > output.fas bp_seqret db.fa:seq1 output.fas bp_seqret db.fa:seq1 -o output.fas bp_seqret -db db.fa…

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Ubuntu Manpage: Bio::Tools::Run::Alignment::Gmap – Wrapper for running gmap.

Provided by: libbio-perl-run-perl_1.6.9-2_all NAME Bio::Tools::Run::Alignment::Gmap – Wrapper for running gmap. SYNOPSIS use Bio::Tools::Run::Alignment::Gmap; use Bio::SeqIO; my $sio = Bio::SeqIO->new(-file=>$filename ,-format=>’fasta’); my @seq; while(my $seq = $sio->next_seq()){ push @seq,$seq; } my $mapper =Bio::Tools::Run::Gmap->new(); my $result = $mapper->run(\@seq); DESCRIPTION Bioperl-run wrapper around gmap. See <www.gene.com/share/gmap/&gt; for information about gmap. It requires a…

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Ubuntu Manpage: Bio::WebAgent – A base class for Web (any protocol) access

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::WebAgent – A base class for Web (any protocol) access SYNOPSIS # This is a abstract superclass for bioperl modules accessing web # resources – normally you do not instantiate it but one of its # subclasess. DESCRIPTION This abstract superclass is a subclass of LWP::UserAgent…

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Ubuntu Manpage: Bio::Search::HSP::HSPFactory – A factory to create Bio::Search::HSP::HSPI objects

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::Search::HSP::HSPFactory – A factory to create Bio::Search::HSP::HSPI objects SYNOPSIS use Bio::Search::HSP::HSPFactory; my $factory = Bio::Search::HSP::HSPFactory->new(); my $resultobj = $factory->create(@args); DESCRIPTION This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser…

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Ubuntu Manpage: Bio::Tools::Run::StandAloneNCBIBlast – Object for the local execution of the NCBI BLAST

Provided by: libbio-perl-run-perl_1.7.3-8_all NAME Bio::Tools::Run::StandAloneNCBIBlast – Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. SYNOPSIS # Do not use directly; see Bio::Tools::Run::StandAloneBlast DESCRIPTION See Bio::Tools::Run::StandAloneBlast FEEDBACK Mailing Lists User feedback is an integral part of the evolution of…

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Ubuntu Manpage: Bio::AlignIO::psi – Read/Write PSI-BLAST profile alignment files

Provided by: libbio-perl-perl_1.6.923-1_all NAME Bio::AlignIO::psi – Read/Write PSI-BLAST profile alignment files SYNOPSIS This module will parse PSI-BLAST output of the format seqid XXXX DESCRIPTION This is a parser for psi-blast blocks. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send…

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Bio::Structure::IO::pdb – PDB input/output stream

Bio::Structure::IO::pdb – PDB input/output stream It is probably best not to use this object directly, but rather go through the Bio::Structure::IO handler system. Go: $stream = Bio::Structure::IO->new(-file => $filename, -format => ‘PDB’); while (my $structure = $stream->next_structure) { # do something with $structure } This object can transform Bio::Structure objects…

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What is Bioconductor in R ?

Bioconductor is an open-source and open-development software project. It provides tools, packages, and resources for the analysis and comprehension of genomic data. Focuses on the statistical analysis and interpretation of high-throughput biological data. These packages include preprocessing, quality control, normalization, differential expression analysis, pathway analysis, genomic annotation, visualization, and machine…

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Bioinformatics Analyst II – Seibold Lab job with National Jewish Health

The Seibold Laboratory is a cutting-edge, NIH funded, laboratory focused on elucidating the pathobiological basis of asthma and other complex lung and allergic diseases. Our goal is to discover pathobiological subgroups of disease (termed disease endotypes) and the genetic, environmental, and immune factors driving their development. We are accomplishing these…

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Bioinformatics CV example + guide [Get top jobs]

Are you looking for your next opportunity in bioinformatics? Then you need a strong CV that showcases your relevant qualifications and experience in the field. In this guide, we’ll teach you how to create an impressive application that showcases your top achievements. You can also check out our bioinformatics CV…

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What Are The Most Common Stupid Mistakes In Bioinformatics?

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

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Ubuntu Manpage: Bio::Installer::Clustalw – DESCRIPTION of Object

Provided by: libbio-perl-run-perl_1.6.9-3_all NAME Bio::Installer::Clustalw – DESCRIPTION of Object SYNOPSIS Give standard usage here DESCRIPTION Describe the object here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation…

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SRM University Digital Repository: PERL PROGRAMMING AND BIOPERL

Search DSpace Advanced Search Home   Browse Communities& Collections Issue Date Author Title Subject   Sign on to: Receive emailupdates My DSpaceauthorized users Edit Profile   Help About DSpace SRM University Digital Repository > Question Papers >…

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Ubuntu Manpage: Bio::DB::Flat::BDB::swiss – swissprot adaptor for Open-bio standard BDB-indexed flat file

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::DB::Flat::BDB::swiss – swissprot adaptor for Open-bio standard BDB-indexed flat file SYNOPSIS See Bio::DB::Flat. DESCRIPTION This module allows swissprot files to be stored in Berkeley DB flat files using the Open- Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use…

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Prokka installation – compilation aborted

Prokka installation – compilation aborted 0 Hi, I installed Prokka using this code posted at github.com/tseemann/prokka sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl sudo cpan Bio::Perl git clone github.com/tseemann/prokka.git $HOME/prokka $HOME/prokka/bin/prokka –setupdb All the steps worked pretty well except the last line for database indexing $HOME/prokka/bin/prokka –setupdb I…

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Ubuntu Manpage: Bio::Structure::StructureI – Abstract Interface for a Structure objects

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Structure::StructureI – Abstract Interface for a Structure objects SYNOPSIS Give standard usage here DESCRIPTION Describe the interface here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing…

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Bio::Network::Interaction – describes a protein-protein interaction

Bio::Network::Interaction – describes a protein-protein interaction # Add an interaction with some attributes use Bio::Network::Interaction; my $interx = Bio::Network::Interaction->new(-weight => $score, -id => $id); $gr->add_interaction(-nodes => [($node1,$node2)], -interaction => $interx); # Retrieve an interaction using an identifier my $interaction = $gr->get_interaction_by_id($id); my $id = $interaction->primary_id; my $wt = $interaction->weight; my…

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Ubuntu Manpage: Bio::AlignIO::nexus – NEXUS format sequence input/output stream

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::AlignIO::nexus – NEXUS format sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; my $in = Bio::AlignIO->new(-format => ‘nexus’, -file => ‘aln.nexus’); while( my $aln = $in->next_aln ) { # do something with the alignment } DESCRIPTION…

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Ubuntu Manpage: Bio::PopGen::IO::phase – A parser for Phase format data

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::PopGen::IO::phase – A parser for Phase format data SYNOPSIS # Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => ‘phase’, -file => ‘data.phase’); # Some IO might support reading in a population at a time my @population; while( my…

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Ubuntu Manpage: Bio::Location::CoordinatePolicyI – Abstract interface for objects implementing a certain

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Location::CoordinatePolicyI – Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print “Location of feature “, $feature->primary_tag(), ” employs a “, ref($location->coordinate_policy()),…

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Ubuntu Manpage: Bio::Tools::Run::Phylo::Phylip::Base – Base object for Phylip modules

Provided by: libbio-perl-run-perl_1.7.1-3_all NAME Bio::Tools::Run::Phylo::Phylip::Base – Base object for Phylip modules SYNOPSIS # Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules DESCRIPTION This module is just a base object for Bioperl Phylip wrappers. IMPORTANT PHYLIP VERSION ISSUES By default…

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Index of ftp://debian.ustc.edu.cn/fink/

binutils-2.31.1.tar.xz   59.00b   August 17 2018 binutils-2.32.tar.xz   57.00b   February 8 2019 at 19:01 bio-svgenes-0.3.3.gem   58.00b   August 30 2013 bio-svgenes-0.4.1.gem   58.00b   September 2 2015 biogrep-1.0.tar.gz   55.00b   September 2 2015 bioinfo-0.1.2.tar.gz   57.00b   September 2 2015 biom-format-1.1.2.tar.gz   61.00b   July 10 2013 biom-format-1.2.0.tar.gz   61.00b   October 15 2013 biom-format-2.1.3.tar.gz   61.00b   September 2 2015 biom-format-2.1.7.tar.gz   61.00b   November…

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Index of ftp://gentoo.kiev.ua/distfiles/

Bio-Graphics-2.39.tar.gz   1.09Mb   July 31 2014 Bio-SamTools-1.39.tar.gz   323.75Kb   August 29 2013 Bio-SamTools-1.41.tar.gz   330.81Kb   December 22 2014 BioPerl-1.6.901.tar.gz   11.72Mb   May 19 2011 BioPerl-DB-1.006900.tar.gz   481.25Kb   December 11 2010 BioPerl-Network-1.006900.tar.gz   2.10Mb   April 21 2011 BioPerl-Run-1.006900.tar.gz   13.87Mb   April 21 2011 Birth-gkrellm.tar.gz   25.48Kb   January 15 2002 Bit-Vector-6.4.tar.gz   128.85Kb   October 3 2004 Bit-Vector-7.2.tar.gz   134.59Kb   March 9 2012…

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SCRMshaw Enrich: Undefined symbol: Perl_xs_boot_epilog

I’m using SCRMshaw to predict CRMs and I’m trying to use the enrichment bash script that comes with it. At first it had the problem of Can’t locate Bio/SeqIO.pm in @INC but this was fixed by exporting the path to a BioPerl installation in an Anaconda environment I made for…

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prokka –setupdb issue

prokka –setupdb issue 0 i wish to do gene annotation using prokka on my linux environment. but i am getting the following thing only instead of answer. i dont know where i made mistake. The command i used: prokka –outdir /home/prokkareport /home/annotation/finalized_contig_fasta the result :[20:43:37] This is prokka 1.14.5 [20:43:37]…

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Ubuntu Manpage: Bio::PopGen::IO::prettybase – Extract individual allele data from PrettyBase format

Provided by: libbio-perl-perl_1.7.2-3_all NAME Bio::PopGen::IO::prettybase – Extract individual allele data from PrettyBase format SYNOPSIS Do not use directly, use through the Bio::PopGen::IO driver DESCRIPTION This object will parse comma delimited PrettyBase output. PrettyBase is defined by the SeattleSNPs pga.gs.washington.edu/ This is expected to be tab delimited (you can vary with…

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Debian — Details of source package bioperl in sid

Links for bioperl Debian Resources: Maintainers: External Resources: The following binary packages are built from this source package: bioperl herramientas de Perl para biología molecular computacional libbio-perl-perl BioPerl core perl modules Other Packages Related to bioperl adep: debhelper-compat (= 13) Package not available adep: libmodule-build-perl framework for building and installing…

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Difference between python and biopython

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

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Ubuntu Manpage: Bio::Factory::SequenceFactoryI – This interface allows for generic building of sequences

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::Factory::SequenceFactoryI – This interface allows for generic building of sequences in factories which create sequences (like SeqIO) SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my $seqbuilder = Bio::Seq::SeqFactory->new(‘-type’ => ‘Bio::PrimarySeq’); my $seq =…

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Ubuntu Manpage: Bio::Tools::Primer::Pair – two primers on left and right side

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Primer::Pair – two primers on left and right side SYNOPSIS use Bio::Tools::Primer::Pair; my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp); # helper functions print “GC percentage different”,$pf->gc_difference(),”\n”; print “product length is “,$pf->product_length,”\n”; DESCRIPTION Primer Pairs represents one primer in a primer pair. This…

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Ubuntu Manpage: Bio::Search::GenericStatistics – An object for statistics

Provided by: libbio-perl-perl_1.7.7-2_all NAME Bio::Search::GenericStatistics – An object for statistics SYNOPSIS my $void = $obj->set_statistic(“statistic_name”,”statistic_value”); my $value = $obj->get_statistic(“statistic_name”); DESCRIPTION This is a basic container to hold the statistics returned from a program. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl…

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Bp_multi_hmmsearch.pl Command – Laramatic

bp_multi_hmmsearch.pl BioPerl wrappers: scripts Maintainer: Debian Med Packaging Team Section: science Install bp_multi_hmmsearch.pl Debian apt-get install bioperl-run Click to copy Ubuntu apt-get install bioperl-run Click to copy Kali Linux apt-get install bioperl-run Click to copy Raspbian apt-get install bioperl-run Click to copy Share Installing bp_multi_hmmsearch.pl command is simple. just copy…

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BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)

BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 There is a newer version of BioPerl Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Accessing BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 To load the module for BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 please use this command…

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[Internship] Bioinformatics Intern, Fall 2022 at Harmonic Discovery (United States)

About Us Based in NYC, Harmonic Discovery is a biotechnology company leveraging biology, medicinal chemistry, and machine learning to create a new generation of therapeutics for oncology and autoimmune disorders. We look for passionate innovators, radical thinkers, and collaborative builders. It’s time to integrate our understanding of biology and chemistry…

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Index of /debian-ubuntu/ubuntu/pool/universe/b/bioperl-run

Name Last modified Size Description Parent Directory   –   bioperl-run_1.6.9-2.debian.tar.gz 2013-11-15 15:13 9.1K   bioperl-run_1.6.9-2.dsc 2013-11-15 15:13 1.6K   bioperl-run_1.6.9-2_all.deb 2013-11-15 15:33 41K   bioperl-run_1.6.9-3.debian.tar.xz 2015-07-03 08:23 8.7K   bioperl-run_1.6.9-3.dsc 2015-07-03 08:23 2.2K   bioperl-run_1.6.9-3_all.deb 2015-07-03 08:43 39K   bioperl-run_1.6.9.orig.tar.gz 2011-06-19 02:04 14M   bioperl-run_1.7.1-3.debian.tar.xz 2017-01-13 15:13 12K  …

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Ubuntu Manpage: Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Map::OrderedPosition – Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = Bio::Map::OrderedPosition->new(-order => 1, -positions…

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man Bio::SeqIO::fasta (3): fasta sequence input/output stream

Bio::SeqIO::fasta(3) fasta sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION This object can transform Bio::Seq objects to and from fasta flat file databases. FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules….

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Ubuntu Manpage: Bio::Tools::Seg – parse “seg” output

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Seg – parse “seg” output SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => ‘seg.fasta’); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, ” is low complexity\n”; } } DESCRIPTION “seg” identifies low-complexity regions on a protein sequence. It is…

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segregating sites calculation fails on gapped sequences #132

Cjfields Author Name: Jason Stajich (@hyphaltip) Original Redmine Issue: 3328, redmine.open-bio.org/issues/3328 Original Date: 2012-02-17 Original Assignee: Bioperl Guts I am Cheng-Ruei Lee, a graduate student in Duke Biology. I’m analyzing many DNA alignments of a plant species. I first used (Bio::PopGen::Utilities -> aln_to_population()) to read in the fasta format alignment,…

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HSP object suitable for describing WABA alignments

Bio::Search::HSP::WABAHSP(3) HSP object suitable for describing WABA alignments SYNOPSIS # use this object as you would a GenericHSP # a few other methods have been added including state DESCRIPTION This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA…

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man Bio::TreeIO::nhx (3): TreeIO implementation for parsing

Bio::TreeIO::nhx(3) TreeIO implementation for parsing SYNOPSIS # do not use this module directlyuse Bio::TreeIO;my $treeio = Bio::TreeIO->new(-format => ‘nhx’, -file => ‘tree.dnd’);my $tree = $treeio->next_tree; DESCRIPTION This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format. FEEDBACK Mailing Lists User feedback is an integral part of the evolution…

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man Bio::AlignIO::selex (3): selex sequence input/output stream

Bio::AlignIO::selex(3) selex sequence input/output stream SYNOPSIS # Do not use this module directly. Use it via the L<Bio::AlignIO> class.use Bio::AlignIO;use strict;my $in = Bio::AlignIO->new(-format => ‘selex’,-file => ‘t/data/testaln.selex’);while( my $aln = $in->next_aln ) {} DESCRIPTION This object can transform Bio::Align::AlignI objects to and from selex flat file databases. FEEDBACK Support…

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bioperl : Impish (21.10) : Ubuntu

 The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. . The recommended packages are needed to run some of the included binaries, for a detailed…

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man Bio::Tools::Phylo::Molphy (3): parser for Molphy output

Bio::Tools::Phylo::Molphy(3) parser for Molphy output SYNOPSIS use Bio::Tools::Phylo::Molphy;my $parser = Bio::Tools::Phylo::Molphy->new(-file => ‘output.protml’);while( my $r = $parser->next_result ) {# r is a Bio::Tools::Phylo::Molphy::Result object# print the model nameprint $r->model, “n”;# get the substitution matrix# this is a hash of 3letter aa codes -> 3letter aa codes representing# substitution ratemy $smat…

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linux – How to fix Perl from anaconda not installing bioperl? Bailing out the installation for BioPerl

vep -i examples/homo_sapiens_GRCh38.vcf –database Can’t locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/modules /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0 /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2 /home/youssef/anaconda3/envs/ngs1/lib/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/5.26.2 .) at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. Compilation failed in require at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm…

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man Bio::MapIO::mapmaker (3): A Mapmaker Map reader

Bio::MapIO::mapmaker(3) A Mapmaker Map reader SYNOPSIS # do not use this object directly it is accessed through the Bio::MapIO system use Bio::MapIO;my $mapio = Bio::MapIO->new(-format => “mapmaker”,-file => “mapfile.map”);while ( my $map = $mapio->next_map ) { # get each mapforeach my $marker ( $map->each_element ) {# loop through the markers…

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man Bio::Root::Version (3): provide global, distribution-level versioning

Bio::Root::Version(3) provide global, distribution-level versioning SYNOPSIS package Bio::Tools::NiftyFeature;require Bio::Root::RootI;# later, in client code:package main;use Bio::Tools::NiftyFeature 3.14;## alternative usage: NiftyFeature defines own $VERSION:package Bio::Tools::NiftyFeature;my $VERSION = 9.8;# later in client code:package main;# ensure we’re using an up-to-date BioPerl distributionuse Bio::Perl 3.14;# NiftyFeature has its own versioning scheme:use Bio::Tools::NiftyFeature 9.8; DESCRIPTION This…

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Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

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biojs – Github Plus

Try to be as detailed as possible. Why do you need it? What data does it use? What should the user experience? ABI file parser –> read .abi files into JSON. We have chromatogram files. Would be great to be able to view these in the browser. Some other .abi…

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BioPerl dependency check always succeeds

In the dependency checking script, the bash builtin command -v is used for checking whether BioPerl is installed. However, this command will always succeed as long as Perl is installed, as it does not execute the command. Consider changing e.g., github.com/abhijeetsingh1704/AcetoScan/blob/70f0428e4fffbff6af17ce5a83b26ce24abd0f29/AcetoScan_MacOS/scripts/AcetoScan_software_check.sh#L48 into if ! perl -MBio::SeqIO -e ‘printf “%vdn”, $Bio::SeqIO::VERSION,…

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awitney/bioperl-run – githubmemory

$Id$ o Version This is bioperl-run version 1.5.2, a developer release. o Description bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common bioperl objects. See the Changes file for more information about what is contained in here. o…

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Biopython Seqio.Index() And Seqio.Index_Db() Very Slow For Large Sequence

Before switching to Biopython, I thought there are similar indexing features in biopython as in bioperl. However, the biopython SeqIO.index_db() and SeqIO.index() methods are so inefficient that it’s almost impossible to random access a segment of genomic sequence using biopython. I tested the performance of biopython and bioperl in retrieving…

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main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

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Rewriting perl code using bioperl

Code: #!/usr/bin/perl use strict; use warnings; die “Usage: $0 <fasta_file style=”box-sizing: border-box; color: rgb(102, 102, 102); font-family: ‘Open Sans’, sans-serif; font-size: 13px; font-style: italic; line-height: 20px; background-color: rgb(251, 251, 251);”><coord_file style=”box-sizing: border-box;”>n” unless @ARGV > 0; my ($fasta_file, $coord_file) = @ARGV; open FASTA, “<” . $fasta_file; my $seq_id; my $dna_string =…

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Any tools converting Genbank format to GFF3 format?

Any tools converting Genbank format to GFF3 format? 4 Dear all, As my title describe, I am asking help to convert Genbank format to GFF format.  By GOOGLing, I found a perl script bp_genbank2gff3.pl), which has many bioperl dependencies.  Could anyone inform me other easy-to-use tools?  Any suggestions will be…

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biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

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Tools To Calculate Average Coverage For A Bam File?

Tools To Calculate Average Coverage For A Bam File? 12 I would like to get the average coverage of all the captured bases in a bam file. What would be the best way to do this? What I am looking is a simple one number like 40X. Given that there…

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Line length limit on input FASTA file: 65,536 characters (limit imposed by bioperl)

Hello, I’m trying to run the following command: agat_sp_extract_sequences.pl -g JU2526_Y39G10AR.22.gff -f JU2526*_region.fa -p And it throws the following error: ————- EXCEPTION: Bio::Root::Exception ————- MSG: Each line of the file must be less than 65,536 characters. Line 2 is 67824 chars. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK:…

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Accepted bioperl-run 1.7.3-7 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 18:52:51 +0200 Source: bioperl-run Architecture: source Version: 1.7.3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: bioperl-run (1.7.3-7) unstable; urgency=medium . * d/watch: fix broken link to github and adjust…

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Difficulty installing Bioperl for use with GUIDANCE

Difficulty installing Bioperl for use with GUIDANCE 0 Hi, I am trying to use the Guidance software to analyze a set of 427 sequences. I have the software downloaded and installed the modules indicated in the Guidance user guide (Perl/BioPerl/Ruby), but when I attempt to run Guidance with the following…

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Can’t locate Bio/SeqIO.pm – path error?

Can’t locate Bio/SeqIO.pm – path error? 0 Hi, I am trying to run snippy on my UBUNTU18 (inside a conda env that has this tool installed) but am getting an error: Can’t locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO.pm module) I checked the posts here, and…

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Ubuntu Manpage: Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl

Provided by: libbio-procedural-perl_1.7.4-2_all NAME Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl VERSION version 1.7.4 SYNOPSIS See Bio::Perl for examples. DESCRIPTION The code in this distribution focuses on simple low-dependency procedural interfaces to BioPerl that don’t require knowledge of BioPerl classes and methods. FEEDBACK Mailing lists User feedback is an…

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Bioperl SeqIO.pm cannot be found

Hello, I am trying to run this command line in the terminal from Mac OS, which is copied from a protocol: FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript> However, I get the following error: command not found, probably because I am not using perl, so I…

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