SNPhylo

Description

snphylo website

Phylogenetic tree is a good tool to infer evolutionary relationships among various organisms so the tree has been used in many evolutionary studies. Consequently, phylogenetic tree based on SNP data have been determined in resequencing projects. However, there was no simple way to determine phylogenetic tree with the huge number of variants determined from resequencing data. Thus, we had developed new pipeline, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data. This module sets the following environment variables:

Environment Modules

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

Environment Variables

• HPC_SNPHYLO_DIR - installation directory
• HPC_SNPHYLO_IMAGE - container image path

Citation

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

Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15(1).

Categories

biology, phylogenetics