Mowgli: a phylogenetic tree reconciliation program

Mowgli (v2): A fast tree reconciliation program allowing to account for ecology traits

Tree reconciliation is a computational approach to explain the discrepancy between two trees such as a gene and a species tree or between a parasite and a host tree. A reconciliaiton postulates a number of evolutionary events such as speciations, duplications, transfers and losses. This approach has important applications in ecology and biogeography but also in genomics to estimate evolutionary scenarios that shaped the content of contemporary genomes and to infer orthology relationships between sequences.

Mowgli runs fast and exact reconciliaiton algorithm. It optimizes a parsimony criterion according to a model that incorporates (co)speciations, duplications, losses and transfers (host-switches).

How to cite

Please cite this software using [1] for the reconciliation algorithm, then [2] or [3,4] depending on the options you use.

Accounting for ecological traits [2]

When dealing with ecological data (e.g. a host and a parasite tree), Mowgli can account for constraints such as geography that limit the set of possible scenarios to those consistent with this information. The "-a", "-y" and "-i" options have been added to Mowgli to handle (geographical) data that have to be in accordance between nodes of the two trees mapped together by the reconciliation. See [2] and Mowgli's manual for more details.

Considering gene tree uncertainty [3,4]

MowgliNNI takes into consideration that gene trees can be partly erroneous due to sequence alignment problems or phylogenetic reconstruction artifacts such as long branch attraction. Thus, it applies Nearest Neighbor Interchange (NNI) edit operations on the edges whose support is lower than a user-chosen threshold to search for a gene tree rearrangement that minimizes the total reconciliation cost according to a given binary species tree. This facility is embedded in the Mowgli program and is called by indicating "-n 1" together with the "-T" option followed by a number to indicate the support threshold under wich an edge is considered as weakly supported.

Download Mowgli

Click here to download the latest version of Mowgli as a compressed archive containing: Click here to download the previous version of Mowgli.

Displaying reconciliations

The SylvX software allows to visualize and edit reconciliations computed by Mowgli. It acts in close interaction with Mowgli to compute reconciliations, e.g. by changing the cost of individual events.

References

[1] J-P. Doyon, C. Scornavacca, K. Y. Gorbunov, G. Szollosi, V. Ranwez, and V. Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers.
RECOMB-CG, 2010. (paper and slides)

[2] V. Berry, J.-P. Doyon, F. Chevenet, E. Jousselin. A geography aware reconciliation method to investigate host/parasite cospeciation.
Mol. Ecol. Resour., 18(5) pp 1173-1184, doi: 10.1111/1755-0998.12897, 2018.

[3] T.H. Nguyen, J.-P. Doyon, S. Pointet, A.-M. Arigon Chifolleau, V. Ranwez, V. Berry. Accounting for gene tree uncertainties improves gene trees and reconciliation inference.
Proc. of the 12th Workshop on Algorithms in Bioinformatics (WABI'12), LNBI 7534, 123-134, Springer, 2012.

[4] T-H. Nguyen, V. Ranwez, S. Pointet, A-M A. Chifolleau, J-P. Doyon and V. Berry. Reconciliation and local gene tree rearrangement can be of mutual profit.
Algorithms for Molecular Biology 2013, 8:12.

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