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
Jonathan Eisen's Lab 
I enjoy the program, it seems to work well. One question when trying to incorporate it into raxml runs: raxml -a option requires integer values and ZORRO provides rational numbers. How does one solve this issue? It isn’t made plain in the publication or in any google search readings. Thanks again!
LikeLike
Will forward this to Martin Wu …
LikeLike
Thank you very much, appreciate the prompt reply
LikeLike
What type of input file is needed? I tried an aligned fasta file, but keep getting errors.
LikeLike
You should probably contact Martin Wu directly. His email is mwu2000 at gmail dot com
LikeLike