Tag Archives: Computational Biology

Perl As Programming Language of Choice for Biologists!!

Perl as Programming Language of Choice for Biologists!!

Posted on 28 October 2013

Why Biologists (Bioinformaticians or Bioinformaticists, if the scientific jargon is to be preferred) Prefer Perl?

I am a bioinformaticist, and love Perl over all other computer languages when it comes to programming in biology. This is not only my case, majority of the biologists prefer Perl for their bioinformatics’ tasks. Perl can be given the status of being the mainstay programming language in the field of Bioinformatics (sometimes known as Computational Biology). There must be some reasons why this is the case; actually there are some very strong points that favor the use of Perl in biology over the other lot of available programming languages. But, to be honest, at times, other computer programming languages can be of more benefit than Perl, at least for a specific task. If you are not acquainted with Perl, click here for, what the heck is Perl? In this article, I will explain why it is justified to consider Perl as programming language of choice for biologists, and for the sake of information, I would like to tell that even the non-biologists too prefer it much!

Continue reading

Bioinformatics and Charles Darwin – Biological Approach of the New Age

Updated 27 December 2014

Bioinformatics and Charles Darwin – Biological Approach of the New Age

Bioinformatics and Charles Darwin – adidarwinian

Bioinformatics and Charles Darwin – Great Great Great – It’s For Mr. Darwin Once Again!!

Continue on the radical path paved by the greatest biologist ever born – Charles Darwin – How can an evolutionary biologist do that?

Bioinformatics, sometimes known as Computational Biology, is presently the best way to study the ever interesting field of evolutionary biology. Bioinformatics provides many unique and powerful tools to study evolutionary biology. One such Bioinformatics tool that I would like to mention here is PHYLIP (the PHYLogeny Inference Package).

PHYLIP is a free software package which consists of many simple yet powerful programs for inferring phylogenies. PHYLIP can be easily downloaded through the Internet.

Classification of the Programs in the PHYLIP package   

Programs included in the PHYLIP package can be enlisted by the type of data or by the type of algorithm used.

Based On The Type Of Data – DNA sequences; Protein sequences; Distance matrices; Quantitative characters;  Restriction sites; Discrete characters; Tree plotting, consensus trees, tree distances and tree manipulation; and Gene frequencies

Based On The Type Of Algorithm – Branch-and-bound tree search; Heuristic tree search; Interactive tree manipulation; Converting data, making distances or bootstrap replicates; and Plotting trees, consensus trees, tree distances

Books To Read —

Bioinformatics For Dummies by Jean-Michel Claverie

Developing Bioinformatics Computer Skills: An Introduction to Software Tools for Biological Applications by Cynthia Gibas

Introduction to Bioinformatics by Arthur Lesk

Practical Computing for Biologists by Steven H. D. Haddock