Dear Ravi kanth, PHP is mainly a hypertext language (PHP is also known as Hypertext PreProcessor) and it is actually influenced by C++ and PERL so, now a days it is majorly used for the server side scripting for web development so, it can be used for the online tool development. Where as PERL (Practical extraction and Reporting Language) is one of the major High level language which is similar to C++, Python. Perl is widely used for development many Biological tools and application as we can develop offline as well as online (using PERL + CGI) tools. PERL has many advantages in Biological programming as it has range of Modules which are a part of BioPerl Module. using Bioperl coding is much easier and better in case of Biological tools and application development. so, that is the major reason for Perl's popularity.

The two languages have different purposes, PERL is general purpose scripting language and PHP mainly for server-side programming.

So for serious programming tasks use PERL (or a "real" programming language like C, C++ or Java) that you can call from your web-tool and for generating HTML code on a web server and implementing the web-tool use PHP.

PERL and PHP have different strengths and you should use them for what they were developed for. PHP had its origins in web and since then has grown in scope but still its strength lies in its ease of in lining PHP code in HTML.

For the most part PERL's strength lies in text processing through regular expression and since then languages have adopted the PERL Compliant Regular Expression (PCRE) as the way to implement regular expressions.

You should be mindful that you should test the accuracy of the mathematical operations used in the language(rounding, etc). For the most part you should also test the underlying algorithm for speed when using regular expressions, HMM's, Levenshtein edit distance, etc. in bioinformatics if you are going to do long batches.

It all boils down to the underlying algorithm implementation.

I have recently started coding in few years and found PHP as far more powerful yet easy for development of tools. only problem is perl is used by most bioinformatician and so many tools and libraries are available. PHP on the other hand, gives the power of generation of every tool possible with very less codes. Ofcourse, as many tools are not available in PHP, its just a leap of faith. I am currently developing a library for chromosome map generation in PHP. in perl it is already available. But the documentation is tough, understanding someone else's documentation is always tough. understanding perl functions inside the libraries increases complexity manifolds. While PHP not only is easy, dyanamic and powerful, many free hosting services are available for PHP as compared to perl which is one of my concern as every institute may not afford to have costly server and high speed internet. Thus we rely on 3rd party free hostings to accomodate low funding consitions. Owing to all these limitations I started following new path of PHP preference over perl. One more thing, if you are dealing with servers that donot produce api and so custom scraping should be involved, PHP will help you a lot over perl.

Note- There are very less scientists who understand that choice of compiler doesnt limit your creativity. Most people know perl as bioinformaticians choice and so they percieve it as perl is only language that proves proficiency. So expertise in PHP may not make you qualified enough for many jobs in future.