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phame website  

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.

Environment Modules

Run module spider phame to find out what environment modules are available for this application.

System Variables

  • HPC_PHAME_DIR - installation directory
  • HPC_PHAME_BIN - executable directory


If you publish research that uses phame you have to cite it as follows:

Sanaa Afroz Ahmed, Chien-Chi Lo, Po-E Li, Karen W Davenport, Patrick S.G. Chain