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Install bioperl with Homebrew, apt

Perl tools for bioinformatics, genomics and life science. Version 1.7.8 via Homebrew; verified from local package data. Also installable with debian: sudo apt install bioperl.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install bioperl

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install bioperl

Debian stable package indexes · bioperl · source: deb.debian.org

overview

Package summary

Perl tools for bioinformatics, genomics and life science

Commands and aliases

  • bp_aacomp
  • bp_bioflat_index
  • bp_biogetseq
  • bp_dbsplit
  • bp_extract_feature_seq
  • bp_fastam9_to_table
  • bp_fetch
  • bp_filter_search
  • bp_find-blast-matches
  • bp_gccalc
  • bp_genbank2gff3
  • bp_index
  • bp_local_taxonomydb_query
  • bp_make_mrna_protein
  • bp_mask_by_search
  • bp_mrtrans
  • bp_mutate
  • bp_nexus2nh
  • bp_nrdb
  • bp_oligo_count
  • bp_process_gadfly
  • bp_process_sgd
  • bp_revtrans-motif
  • bp_search2alnblocks
  • bp_search2gff
  • bp_search2table
  • bp_search2tribe
  • bp_seq_length
  • bp_seqconvert
  • bp_seqcut
  • bp_seqpart
  • bp_seqret

history

Project history and usage

BioPerl is the long-running Perl bioinformatics toolkit: a broad collection of modules and scripts for sequences, formats, alignments, database access, and interfaces to life-science programs.

Project history

BioPerl's own history article traces the project to the VSNS-BCD BioComputing Courses and early Perl bioinformatics work in the mid-1990s, with contributors from genome centers including Stanford, Washington University, and the Sanger Centre. The article describes production use at those sites and the project's association with Open Bioinformatics Foundation activity.

The project moved through the 0.7 release work in 2000-2001, held Open Bio Hackathon activity in 2002, and released BioPerl 1.0 in May 2002 as a significant stable toolkit milestone. The FAQ documents the even-numbered stable release convention and notes the 0.7 series as stable releases from 2001.

The modern bioperl-live GitHub repository was created in May 2010 and is described as the core BioPerl 1.x code. The README explains that the BioPerl distribution provides the foundation for other BioPerl distributions, while related repositories cover additional modules.

Adoption history

BioPerl was adopted by the genome-center and open-bio communities before GitHub-era packaging, and its 2002 Genome Research citation marks it as a recognized scientific software toolkit. The project site calls BioPerl an international association of users and developers of open source Perl tools for bioinformatics, genomics, and life science.

In package-manager culture, BioPerl represents the CPAN-to-distro path of scientific software: installable as Perl modules through CPAN/MetaCPAN and also packaged by Linux distributions and Homebrew according to the input metadata.

How it is used

The README describes BioPerl classes for biological sequences, multiple file formats, sequence alignments, database searching objects, and interfaces to programs such as EMBOSS, ClustalW, and BLAST. The FAQ points users to perldoc, HOWTOs, examples, scripts, and tests as usage references.

Homebrew exposes many `bp_*` command-line scripts, including format conversion, sequence extraction, taxonomy, GFF, alignment, and search-result utilities. That makes the package useful both as a Perl library stack and as a toolbox of small bioinformatics commands.

Why package nerds care

BioPerl is package-nerd significant because it is one of the archetypal domain-specific language ecosystems: Perl plus CPAN plus lots of small scripts, wrapped into a scientific toolkit that predates today's language-specific package-manager norms.

It also shows how research software ages in public. The package carries old Perl idioms, a huge module surface, CPAN distribution semantics, distro packages, GitHub-era issue tracking, and decades of bioinformatics practice in one installable artifact.

Timeline

  • 1996: Early organizational roots in VSNS-BCD BioComputing Courses, according to the BioPerl history article.
  • 2000-2001: Work toward the 0.7 stable release series.
  • 2001: 0.7 stable releases documented by the FAQ.
  • 2002: First Open Bio Hackathon activity and BioPerl 1.0 release.
  • 2002: BioPerl toolkit paper published in Genome Research.
  • 2010: bioperl-live repository created on GitHub.
  • 2019: Current BioPerl website footer and docs generation era visible on bioperl.org.

Related projects

  • BioPerl is related to bioperl-db, bioperl-run, bioperl-experimental, EMBOSS, ClustalW, BLAST, GBrowse, GMOD, CPAN/MetaCPAN, and the Open Bioinformatics Foundation family of projects.

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew bottle metadata was recorded.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
bp_aacompexecutableindexed executableDiscovered from the local executable index.
bp_bioflat_indexexecutableindexed executableDiscovered from the local executable index.
bp_biogetseqexecutableindexed executableDiscovered from the local executable index.
bp_dbsplitexecutableindexed executableDiscovered from the local executable index.
bp_extract_feature_seqexecutableindexed executableDiscovered from the local executable index.
bp_fastam9_to_tableexecutableindexed executableDiscovered from the local executable index.
bp_fetchexecutableindexed executableDiscovered from the local executable index.
bp_filter_searchexecutableindexed executableDiscovered from the local executable index.
bp_find-blast-matchesexecutableindexed executableDiscovered from the local executable index.
bp_gccalcexecutableindexed executableDiscovered from the local executable index.
bp_genbank2gff3executableindexed executableDiscovered from the local executable index.
bp_indexexecutableindexed executableDiscovered from the local executable index.
bp_local_taxonomydb_queryexecutableindexed executableDiscovered from the local executable index.
bp_make_mrna_proteinexecutableindexed executableDiscovered from the local executable index.
bp_mask_by_searchexecutableindexed executableDiscovered from the local executable index.
bp_mrtransexecutableindexed executableDiscovered from the local executable index.
bp_mutateexecutableindexed executableDiscovered from the local executable index.
bp_nexus2nhexecutableindexed executableDiscovered from the local executable index.
bp_nrdbexecutableindexed executableDiscovered from the local executable index.
bp_oligo_countexecutableindexed executableDiscovered from the local executable index.
bp_process_gadflyexecutableindexed executableDiscovered from the local executable index.
bp_process_sgdexecutableindexed executableDiscovered from the local executable index.
bp_revtrans-motifexecutableindexed executableDiscovered from the local executable index.
bp_search2alnblocksexecutableindexed executableDiscovered from the local executable index.
bp_search2gffexecutableindexed executableDiscovered from the local executable index.
bp_search2tableexecutableindexed executableDiscovered from the local executable index.
bp_search2tribeexecutableindexed executableDiscovered from the local executable index.
bp_seq_lengthexecutableindexed executableDiscovered from the local executable index.
bp_seqconvertexecutableindexed executableDiscovered from the local executable index.
bp_seqcutexecutableindexed executableDiscovered from the local executable index.
bp_seqpartexecutableindexed executableDiscovered from the local executable index.
bp_seqretexecutableindexed executableDiscovered from the local executable index.
bp_seqretsplitexecutableindexed executableDiscovered from the local executable index.
bp_split_seqexecutableindexed executableDiscovered from the local executable index.
bp_sreformatexecutableindexed executableDiscovered from the local executable index.
bp_taxid4speciesexecutableindexed executableDiscovered from the local executable index.
bp_taxonomy2treeexecutableindexed executableDiscovered from the local executable index.
bp_translate_seqexecutableindexed executableDiscovered from the local executable index.
bp_tree2pagexecutableindexed executableDiscovered from the local executable index.
bp_unflatten_seqexecutableindexed executableDiscovered from the local executable index.

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-08-03
manager version1.7.8
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:bioperl
Version1.7.8
Package managerHomebrew
Homepagehttps://bioperl.org
Repositoryhttps://github.com/bioperl/bioperl-live
Bottlenot recorded
Servicenone declared

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

bioperl 1.7.8-1

Perl tools for computational molecular biology

http://www.bioperl.org/

sudo apt install bioperl
  • Section: science
  • Architecture: all
  • 3 dependencies
  • 17 optional deps
  • normalized package name match
  • Matched by: Bioperl
Debian stable package indexes · deb.debian.org · Debian stable package indexes: bioperl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

libbio-perl-perl 1.7.8-1

BioPerl core perl modules

http://www.bioperl.org/

sudo apt install libbio-perl-perl
  • Section: perl
  • Architecture: all
  • Source Package: bioperl
  • 3 dependencies
  • 32 optional deps
  • normalized package name match
  • Matched by: Bioperl
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbio-perl-perl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Ubuntu apt95%

bioperl 1.7.8-1

Perl tools for computational molecular biology

http://www.bioperl.org/

sudo apt install bioperl
  • Section: universe/science
  • Architecture: all
  • 3 dependencies
  • 17 optional deps
  • normalized package name match
  • Matched by: Bioperl
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: bioperl from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

libbio-perl-perl 1.7.8-1

BioPerl core perl modules

http://www.bioperl.org/

sudo apt install libbio-perl-perl
  • Section: universe/perl
  • Architecture: all
  • Source Package: bioperl
  • 3 dependencies
  • 32 optional deps
  • normalized package name match
  • Matched by: Bioperl
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbio-perl-perl from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • pkg.so package database
  • pkgdb category and tag curation