#sphere

A scalable phylogenetic tree inference algorithm for SARS-CoV-2 sequences.

java -jar sphere.jar 

Run SPHERE with the following arguments:

  -i:  input path to aligned sequences (fasta file) from nucleotide alphabet {A,C,T,G}, or "N" for missing positions/ambiguities.  
  -r:  input path to reference sequence with no missing positions/ambiguities ({A,C,T,G} only, no N's)  
  -e:  output path for edges (.csv)  
  -v:  output path for vertices (.csv)  
  -s:  output path for gap-filled sequences (.fasta)  

One way to run the sample files would be:

java -jar sphere/sphere.jar -i sample_inputs/jan31.fasta -r sample_inputs/ref.fas -v vertices_out.csv -e edges_out.csv -s sequences_out.csv 

You can run SPHERE with the precompiled jar in the "sphere" folder.

Or, if you have Maven installed on your system, run

mvn clean install

to recompile the source code into a new jar.

Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin Icer, Pavel Skums, and Alex Zelikovsky. Journal of Computational Biology. Nov 2021.1130-1141. http://doi.org/10.1089/cmb.2021.0306