ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
- Sourceforge: ZORRO – probabilistic masking for phylogenetics
Zorro is written primarily by Martin Wu, Sourav Chatterji and Aaron Darling.
A paper describing it was published January 17, 2012 in PLoS One. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288.
More detail can be found in a blog post on “The Tree of Life” blog by Jonathan Eisen: New openaccess paper from my lab on “Zorro” software for automated masking of sequence alignments