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spruceup website  

spruceup is a Python tool for biologists (bioinformaticians, phylogeneticists, evolutionary biologists) doing inference on phylogenomic sequence alignments. It allows discovery and removal of individual poorly aligned sequences or sequence fragments (alignment rows), which is different from the problem of poorly aligned sequence blocks (alignment columns) commonly addressed by alignment trimming software.

Environment Modules

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

System Variables

  • HPC_SPRUCEUP_DIR - installation directory
  • HPC_SPRUCEUP_BIN - executable directory


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

Borowiec, M.L. (2019) Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments. Journal of Open Source Software, 4(42), 1635, https://doi.org/10.21105/joss.01635