DNA Alignment Software | Features

DNA Alignment functions

Aligns both DNA or amino acid data.
Reads formats: FASTA (*.fas, *.txt), TemporaryAlignment (*.ali).
Aligns 1 or multiple sequences under a reference sequence.
Displays alignments and allows editing.
Optional FASTA-import without auto-alignment (i.e. for already aligned data).
Writes formats: Network (*.rdf, *.ami), publication-style tables (*.txt), Sequential Nexus (*.nex), Sequential Phylip (*.phy), FASTA (*.fas, *.txt), TemporaryAlignment (*.ali).

Specifications

Nucleotide position numbering of the reference sequence, including multiple np-ranges in the numbering, is configurable. Example numbering: "15996-16569; 1-576"
Maximal sequence length 99999.
Maximal number of sequences unlimited except by available memory on your computer. NB: Under Windows there is a virtual memory limit which users with huge data sizes could hit, but in practice run time duration will be the first limit.
Hardware requirements: PCs with Windows Vista/XP/NT/2000/98. Alternatively e.g. Mac with Virtual PC Windows emulation. Alternatively new Linux versions with up-to-date(!) WINE windows emulation, e.g. SUSE 10 (note: email hotline support does not cover linux-installation-related questions). Recommendations: RAM 512MB, CPU 1.5GHz or faster.
The alignment algorithm is designed for closely related sequences without large-scale re-arrangements or duplications. Pairwise alignment of each sequence with respect to a user-defined ("reference") sequence. The algorithm is a very sophisticated pairwise alignment algorithm based on the idea in [Morgenstern B et al. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics. 1998;14(3):290-4] with specific improvements in our implementation. Unlike older methods, large segments of sequences are compared and there is no "gap penalty". If more than 1 sequence is aligned, the pairwise alignments with the reference sequence are optimised by comparing multiple sequences.