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.
Install singularity as explained here
Download the singularity image from the above mentioned link
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.
-msa <f> [Required]
File <f> contains a multiple sequence alignment of proteins in fasta format.
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:
Last Update Jan. 2020