Introduction
libseq is a library to manipulate biological sequences (nucleotide or
amino acid sequences).
Goal
This library originated as part of my PhD project, which involves
molecular evolution of HIV, with respect to resistance development
against antiretroviral products.
It provides a limited set of what can be generally found in the
biojava, bioperl and biopython projects, in C++. The scope is however
limited to efficient and simple sequence manipulation. Application
features, such as sequence alignment, are beyond the scope of this
library.
Features
- Nucleotide and AminoAcid sequence class based on std::vector
- Translation from Nucleotide to Aminoacid sequences
- FASTA I/O
- Full support for IUPAC ambiguity symbols
- Simple C++ interface
Status
The current public release (Jul, 17 2006), libseq-0.3.tar.gz,
contains the basic functionality, which was needed so far for my
PhD. It has been exhaustively tested in various projects small and large.
You are welcome to add features you find missing.
Documentation
Installation
I have switched to cmake for the build process, so I am looking forward
to hear from anyone being succesfull to build on anyhthing other than
Linux, and I am especially curious for experiences with Microsoft
development tools ?
There is an install file with build instructions on Linux, which is
follows a standard CMake build and install process.
Reference
Sourceforge
The project is hosted at sourceforge here.