Haplowser was developed to browse haplotypes and their annotations throughout whole genomes (version 1.0.0 as of Jan 24 2009). The software can be run through
Java Web Start(JWS)(recommended) or be downloaded
here with
the sample data. Haplowser is written in JAVA, supporting Windows and Linux. The software is open-source based and its source code is publicly available under the ordinary GNU Public License (GPL). The source code can be downloaded
here.
Unlike other comparative genome browsers, Haplowser provides unique features such as:
Instead of haploid sequences, navigate haplotypes with gene annotations and custom tracks.
Multiple alignments of Haplotypes are displayed at the base level.
After haploid gene sequences are mapped to haplotypes, diploid gene sequences can be saved by using a mouse operation.
Heterozygosity existing at haplotypes is summarized and easily navigated by a user.
All the functions are provided though an intuitive user interface.
A user can create or open project files (*.prj files), each of which consists of a reference genome sequence and aligned genome sequences to the reference genome sequence. The main window is divided into 5 smaller windows: multiple alignment window, alignment plot window, vertical annotation window (for a reference sequence), and horizontal annotation window (for aligned sequences), property window. For more details of Haplowser, please read
the user’s guide.
