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You can learn this relatively easily with textbooks, such as the Perl Cookbook by Tom
Christiansen and Nathan Torkington (2003). This book is just very well written and pro
vides a very good introduction to the PERL programming language.
Or the book Beginning Perl for Bioinformatics by James Tisdall (2001).
There are of course countless tutorials on the net, e.g.
• https://www.perl.org/learn.html
• https://www.tutorialspoint.com/perl/
• https://wiki.selfhtml.org/wiki/Perl
• https://www-cgi.cs.cmu.edu/cgi-bin/perl-man
To be able to program faster in PERL yourself, there are also the BioPerl modules:
• https://en.wikipedia.org/wiki/BioPerl
• https://bioperl.org (is the entry page).
Here are three aspects of such recipes listed as article examples:
Angly FE, Fields CJ, Tyson GW (2014) The Bio-Community Perl toolkit for microbial ecol
ogy. Bioinformatics 30(13):1926–1927. https://doi.org/10.1093/bioinformatics/btu130
Vos RA, Caravas J, Hartmann K et al (2011) BIO: phylo-phyloinformatic analysis using
perl. BMC Bioinformatics 12:63. https://doi.org/10.1186/1471-2105-12-63
Stajich JE, Block D, Boulez K et al (2002) The Bioperl toolkit: Perl modules for the life
sciences. Genome Res 12(10):1611–1618.
Java
This programming language by James Gosling (1991) runs on every major operating sys
tem (“platform”, Windows, Mac and LINUX) and is so popular because you can write it
once and then run it (especially over the Internet) on any platform. It is an object-oriented,
modern programming language, so “objects” as complex concepts are central to it. Java‘s
syntax is similar to C or C++, but Java‘s comfortable, high level language does not make
it as easy to refer to single bit instructions (the machine language) as it is with C or C+ +.
Here, too, there is Biojava, i.e. ready-made program modules for bioinformatics:
And in addition a number of recipes and program modules (routines):
https://biojava.org
https://biojava.org/wiki/Main_Page/
19.6 Introduction to Programming (Meta Tutorial)