Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Open Problems in Parameterized and Exact Computation - IWPEC 2006

In September 2006, the Second International Workshop on Parameterized and Exact Computation was held in Zürich, Switzerland, as part of ALGO 2006. At the end of IWPEC 2006, a problem session was held. (Most of) the problems mentioned at this problem session, and some other problems, contributed by the participants of IWPEC 2006 are listed here

07281 Abstracts Collection -- Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs

From 8th to 13th July 2007, the Dagstuhl Seminar ``Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

LIPIcs, Volume 248, ISAAC 2022, Complete Volume

LIPIcs, Volume 248, ISAAC 2022, Complete Volum