NSS Alignment Format


NSS (Name-Sequence-Sequence) is a sequence alignment format. It's a text format, storing one alignment per line. In case of pairwise alignment each line has 3 tab-separated fields: The first field is the alignment name, the second and third fields are aligned sequences. The name can be empty, in such case the line begins with tab character.


aln1 gataacaggcgtgaac gataacaggtgtgaac aln2 taa--aaaaaaaTAGACTCT taacaaaaaaaaaaGACTCT

It can be naturally extended to multiple alignment: In such case each line would have N+1 fields (where N is the number of aligned sequences).


I first saw this format supported by Dr. Yuichiro Hara's scripts. I then decided to document it and support it in my tools.


The advantages of this format:

Disadvantages of this format:

  © 2014 Kirill Kryukov
This document has been placed in the public domain