Recommended Books:

Bioinformatics : A Practical Guide to the Analysis of Genes and Proteins (2nd Edition)
by Andreas D. Baxevanis, B. F. Francis Ouellette


The book gives an overview of many available computational tools. It focuses on the practical aspects of how to use the programs rather then on how the methods work from theoretical point of view. Good to use as a reference book.
Molecular Evolution : A Phylogenetic Approach
by Roderic D. M. Page, Edward C. Holmes


The book gives excellent introduction to the area of molecular evolution. Does not go deeply into gory details, but gives a good overview of terminology and methods available.
Molecular Evolution
by Wen-Hsiung Li


More advanced text
Beginning Perl for Bioinformatics
by James Tisdall


This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving particular problems or class of problems, so you'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to tackle more advanced bioinformatics programming.
Learning Perl (2nd Edition)
by Randal L. Schwartz, Tom Christiansen


Many tedious and repetitive tasks can be automated with help of Perl. Currently Perl is widely used in the area of bioinformatics. This book is an introductory book on Perl programming and assumes that a reader does not have any programming experience