BioPerl (Perl5)
- BioPerl represents an ecosystem of related molecular biology modules written in the Perl5 programming language
- Supported by the Open Bioinformatics Foundation and includes additional utilities and interfaces for common bioinformatics applications
- Launched in 2002 and has contributed to major scientific achievements including the Human Genome Project
A few equivalent application tools between BioJulia and BioPerl:
| Application | BioJulia packages | BioPerl modules/objects |
|---|---|---|
| Input/Output | FASTX, XAM, BigWig,... | SeqIO |
| Sequence alignment | BioSequences, BioAlignments | AlignIO, SimpleAlign |
| Data structures | Kmers, IntervalTrees | Bio::Kmer, Bio::Tree |
| Population Genetics | PopGen | PopGen |
A few package/ecosystem equivalents between Julia and Perl5:
| Application | Julia | Perl5 |
|---|---|---|
| Data manipulation/analysis | DataFrames, CSV, Query | PDL, Text-CSV |
| Plotting/visualization | Plots, Gadfly, Makie, TidierPlots | GDGraph, Chart-GGPlot |
| Statistical analysis | Statistics, HypothesisTests, GLM | Statistics-Descriptive, PDL-Stats |
| Numerical mathematics | LinearAlgebra, Symbolics | PDL-LinearAlgebra, Math-Symbolic |
| Notebook/report generator | IJulia, Pluto | Devel-IPerl |
| Web applications | Genie, Franklin | Catalyst, Mojolicious |
A few notable differences between Julia and Perl5:
| Julia | Perl5 |
|---|---|
| High-level, general-purpose compiled language | High-level, general-purpose interpreted language |
| Dynamically typed with multiple dispatch and optional type annotations | Dynamically typed without type annotations support |
| Built-in parallelism via threads, coroutines (Tasks) | Parallelism via threads, external modules (Coro, Parallel,...) |
| Lisp-inspired metaprogramming (S-expressions, homoiconicity,...) | Macro-less metaprogramming capabilities (eval, symbol table manipulation,...) |
| Single language implementation (JuliaLang) | Family of related languages/implementations (Perl5, Perl6/Raku, ActivePerl,...) |
To transition from Perl5 to Julia:
- Read the Julia manual for an in-depth look at its internals and features
- See Running External Programs in the manual for running Perl scripts or other programs from Julia