Install bioperl with Homebrew, apt

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

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

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

• https://bioperl.org/
• https://bioperl.org/FAQ.html
• https://bioperl.org/articles/History_of_BioPerl.html
• https://github.com/bioperl/bioperl-live
• https://raw.githubusercontent.com/bioperl/bioperl-live/master/README.md
• source_facts.executables
• source_facts.package-manager