MirrorTree

Predictor of protein interaction partners and functional relationships based on similarity of phylogenetic histories.

References

Florencio Pazos & Alfonso Valencia (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering. 14(9):609-614.
[MedLine:11707606] [HTML] [PDF]
Florencio Pazos, Juan A. G. Ranea, David Juan & Michael J. E. Sternberg. (2005). Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. Journal of Molecular Biology. 352(4):1002-1015.
[PubMed:16139301] [HTML] [PDF] [online additional material]
David Juan, Florencio Pazos & Alfonso Valencia. (2008). High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA. 105(3):934-939.
[PubMed:18199838] [HTML] [PDF] [ECID system]
David Ochoa & Florencio Pazos. (2010). Studying the co-evolution of protein families with the Mirrortree web server. Bioinformatics. 26(10):1370-1371.
[Pubmed:20363731] [HTML] [PDF] [MirrorTree Server]
Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia and Florencio Pazos (2011). Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics. 12:363.
[PubMed:21910884] [HTML] [PDF]

Datasets

Datasets used in these publications are available under request.

Software

Academic versions of this software for different operative systems are available under request. Please contact the address below for any question regarding these programs.

Please note that this software is in academic version and requires some expertise in both, bioinformatics and in computing, to be used. Namely, the multiple sequence alignments of ortholog sequences have to be generated by the user and formated in a given way, and the software is distributed as a command line program without user graphical interface. Non expert users please consider using our recently developed web server for the mirrortree program. It only requires single sequences as input and the results can be inspected in an interactive graphical interface.

Dr. Florencio Pazos Cabaleiro.
Computational Systems Biology Group.
National Center for Biotechnology (CNB-CSIC)
C/Darwin, 3. Cantoblanco. 28049 Madrid. Spain

Tlf. +34.915854669. Fax. +34.915854506