# Install bioperl with Homebrew, apt Perl tools for bioinformatics, genomics and life science. Version 1.7.8 via Homebrew; verified 2026-04-20. ## Install ```sh sudo av install brew:bioperl ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install bioperl ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install bioperl ``` Evidence: Debian stable package indexes: bioperl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Package facts - **Package key:** brew:bioperl - **Package manager:** Homebrew - **Package manager page:** - **Version:** 1.7.8 - **Source summary:** Perl tools for bioinformatics, genomics and life science - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** Artistic-1.0-Perl OR GPL-1.0-or-later - **Source archive:** - **Last updated:** 2026-04-20T03:46:02Z - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - bp_aacomp (cli) - bp_bioflat_index (cli) - bp_biogetseq (cli) - bp_dbsplit (cli) - bp_extract_feature_seq (cli) - bp_fastam9_to_table (cli) - bp_fetch (cli) - bp_filter_search (cli) - bp_find-blast-matches (cli) - bp_gccalc (cli) - bp_genbank2gff3 (cli) - bp_index (cli) - bp_local_taxonomydb_query (cli) - bp_make_mrna_protein (cli) - bp_mask_by_search (cli) - bp_mrtrans (cli) - bp_mutate (cli) - bp_nexus2nh (cli) - bp_nrdb (cli) - bp_oligo_count (cli) - bp_process_gadfly (cli) - bp_process_sgd (cli) - bp_revtrans-motif (cli) - bp_search2alnblocks (cli) - bp_search2gff (cli) - bp_search2table (cli) - bp_search2tribe (cli) - bp_seq_length (cli) - bp_seqconvert (cli) - bp_seqcut (cli) - bp_seqpart (cli) - bp_seqret (cli) - bp_seqretsplit (cli) - bp_split_seq (cli) - bp_sreformat (cli) - bp_taxid4species (cli) - bp_taxonomy2tree (cli) - bp_translate_seq (cli) - bp_tree2pag (cli) - bp_unflatten_seq (cli) - bp_aacomp (alias) - bp_bioflat_index (alias) - bp_biogetseq (alias) - bp_dbsplit (alias) - bp_extract_feature_seq (alias) - bp_fastam9_to_table (alias) - bp_fetch (alias) - bp_filter_search (alias) - bp_find-blast-matches (alias) - bp_gccalc (alias) - bp_genbank2gff3 (alias) - bp_index (alias) - bp_local_taxonomydb_query (alias) - bp_make_mrna_protein (alias) - bp_mask_by_search (alias) - bp_mrtrans (alias) - bp_mutate (alias) - bp_nexus2nh (alias) - bp_nrdb (alias) - bp_oligo_count (alias) - bp_process_gadfly (alias) - bp_process_sgd (alias) - bp_revtrans-motif (alias) - bp_search2alnblocks (alias) - bp_search2gff (alias) - bp_search2table (alias) - bp_search2tribe (alias) - bp_seq_length (alias) - bp_seqconvert (alias) - bp_seqcut (alias) - bp_seqpart (alias) - bp_seqret (alias) - bp_seqretsplit (alias) - bp_split_seq (alias) - bp_sreformat (alias) - bp_taxid4species (alias) - bp_taxonomy2tree (alias) - bp_translate_seq (alias) - bp_tree2pag (alias) - bp_unflatten_seq (alias) ## Build dependencies - pkgconf ## Uses from macOS - expat - libxml2 - perl ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 1.7.8 - Package-manager updated: 2026-04-20 - Local data: ok - Upstream repository: https://bioperl.org - info: Release/tag comparison is only available for GitHub repositories. ## 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. ### Sources - - - - - - source_facts.executables - source_facts.package-manager ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bioperl - **Version Scheme:** 0 - **Revision:** 6 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Debian apt - bioperl - 1.7.8-1: normalized package name match | Debian stable package indexes: bioperl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Perl tools for computational molecular biology | http://www.bioperl.org/ - Debian apt - libbio-perl-perl - 1.7.8-1: normalized package name match | Debian stable package indexes: libbio-perl-perl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | BioPerl core perl modules | http://www.bioperl.org/ - Ubuntu apt - bioperl - 1.7.8-1: normalized package name match | Ubuntu 24.04 LTS package indexes: bioperl from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Perl tools for computational molecular biology | http://www.bioperl.org/ - Ubuntu apt - libbio-perl-perl - 1.7.8-1: normalized package name match | Ubuntu 24.04 LTS package indexes: libbio-perl-perl from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | BioPerl core perl modules | http://www.bioperl.org/ ## Related links - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://www.automicvault.com/pkg/brew-utility-packages/) - Matched Homebrew package provider. - [pkgconf](https://www.automicvault.com/pkg/brew/pkgconf/) - Build dependency declared by Homebrew. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Popular package that depends on this formula. - [vcftools](https://www.automicvault.com/pkg/brew/vcftools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, perl, science. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://www.automicvault.com/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [breseq](https://www.automicvault.com/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [echtvar](https://www.automicvault.com/pkg/brew/echtvar/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [fastga](https://www.automicvault.com/pkg/brew/fastga/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [diamond](https://www.automicvault.com/pkg/brew/diamond/) - Local package facts share a topical domain. Shared terms: bioinformatics, blast, cli, local, protein. ## Combined YAML source View the package source record on GitHub. [combined/bioperl.yml](https://github.com/automic-vault/db/blob/main/combined/bioperl.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph