A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288
The paper describes the software "Zorro" which is used for automated "masking" of sequence alignments. Basically, if you have a multiple sequence alignment you would like to use to infer a phylogenetic tree, in some cases it is desirable to block out regions of the alignment that are not reliable. This blocking is called "masking."
Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome. This "positional homology" is not always easy to assign and for regions where positional homology is ambiguous it may be better to ignore such regions when inferring phylogenetic trees from alignments.
Historically, masking has been done by hand/eye looking for columns in a multiple sequence alignment that seem to have issues and then either eliminating those columns or giving them a lower weight and using a weighting scheme in the phylogenetic analysis.
What Zorro does is it removes much of the subjectivity of this process and generates automated masking patterns for sequence alignments. It does this by assigning 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.
The software is available at Sourceforge: ZORRO – probabilistic masking for phylogenetics. It was written primarily by Martin Wu (who is now a Professor at the University of Virginia) and Sourav Chatterji with a little help here and there from Aaron Darling I think. The development of Zorro was part of my "iSEEM" project that was supported by the Gordon and Betty Moore Foundation.
In the interest of sharing, since the paper is fully open access,