Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary: URec is a software based on a concept of unrooted reconciliation. It can be used to reconcile a set of unrooted gene trees with a rooted species tree or a set of rooted species trees. Moreover, it computes detailed distribution of gene duplications and gene losses in a species tree. It can be used to infer optimal species phylogenies for a given set of gene trees. URec is implemented in C++ and can be easily compiled under Unix and Windows systems. Availability: Software is freely available for download from our website at http://bioputer.mimuw.edu.pl/~gorecki/urec. This webpage also contains Windows executables and a number of advanced examples with explanations. Contact: gorecki@mimuw.edu.pl