External Tools

Sequence Manipulation
Name Description

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.


Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.


A Simplified Web interface to the more popular utilities within the EMBOSS suite of sequence analysis programs.


Package of Programs runnable using web and web-services interfaces.

Restriction Analysis
Name Description
Restriction Site Analysis

List of  useful and interesting web sites for restriction analysis


Restriction Enzyme Database - search for restriction enzymes by name, species, recognition sequence, companies that sell restriction enzymes or by authors and citations associated with each enzyme.


A nice site for generating retriction maps and identification of non-overlapping ORFs.

Primer Design
Name Description

Primer3 is a widely used program for designing PCR primers. Primer3Plus is a web-interface for Primer3


Application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment. The program iteratively runs the Primer3 application for each alignment sequence and collates the results.

RT-Primer Design

Real Time PCR primer design.