Zorro (probabilistic alignment masking)

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.

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

5 Responses to Zorro (probabilistic alignment masking)

  1. Chris says:

    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!


  2. Chris says:

    Thank you very much, appreciate the prompt reply


  3. Jana U'Ren says:

    What type of input file is needed? I tried an aligned fasta file, but keep getting errors.


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