exact comparison of biological sequences

Versions 0.2.2
License GPLv3+

biodiff is a variant caller that determines the exact differences between two biological sequences. It can operate on DNA and protein sequences, as long as they are in fasta format. The sequences to be compared must have the same fasta header (up to the first whitespace). If the reference and query each have only one sequence, however, the header need not match and the comparison will be done, but a warning will be emitted. Output is in the Variant Call Format.


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install biodiff

and update with:

conda update biodiff


A Docker container is available at