A tool to detect clusters of the coevolving positions in a multiple sequence alignment of highly conserved protein sequences



BIS2TreeAnalyzer detects patterns of coevolution over large distance trees, by analyzing closely related subtrees of sequences using BIS2 (Carbone and Dib 2011; Oteri et al. 2017), and combining the subtree results in a principled manner.

Because of the high number of dependencies, the installation process has been simplified using a singularity container technology that has a higher degree of security with respect other commonly used technology.


The singularity BIS2TreeAnalyzer image can be downloaded here.


System requirements:


How to install BIS2TreeAnalyzer:

Install singularity as explained here

Download the singularity image from the above mentioned link


How to excute BIS2TreeAnalyzer:

singularity run BIS2TreeAnalyzer.sif  --msa test/alignment.fasta --dir test/iterativeBIS2

The above command will perform the computation inside test/iterativeBIS2 and write the global result to test/iterativeBIS2/BIS2_CLUSTERS.txt.


Input files:

-msa <f> [Required] 

File <f> contains a multiple sequence alignment of proteins in fasta format.

Data Set:

Input files used in our coevolution analysis performed on the Polymerase protein of the Hepatitis B Virus can be found here:

HBV Pol MSAs for each genotype


For questions, comments, or suggestions feel free to contact Alessandra Carbone or Elin Teppa.



If you use BIS2TreeAnalyzer, please cite:

  • E.Teppa, F.Nadalin, C.Combet, D.Zea, L.David, A.Carbone. Coevolution analysis of amino-acids reveals diversified drug resistance solutions in viral sequences: a case study of Hepatitis B Virus, Virus Evolution, 2020. In press.

Last Update Jan. 2020