Literature DB >> 17182699

URec: a system for unrooted reconciliation.

Pawel Górecki1, Jerzy Tiuryn.   

Abstract

UNLABELLED: 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.

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Year:  2006        PMID： 17182699     DOI： 10.1093/bioinformatics/btl634

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

1.  Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.

Authors:  Laura A Katz; Jessica R Grant; Laura Wegener Parfrey; J Gordon Burleigh
Journal:  Syst Biol       Date:  2012-02-14       Impact factor: 15.683

2.  Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Authors:  J Gordon Burleigh; Mukul S Bansal; Oliver Eulenstein; Stefanie Hartmann; André Wehe; Todd J Vision
Journal:  Syst Biol       Date:  2010-12-24       Impact factor: 15.683

3.  DrML: probabilistic modeling of gene duplications.

Authors:  Paweł Górecki; Oliver Eulenstein
Journal:  J Comput Biol       Date:  2013-09-27       Impact factor: 1.479

4.  Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

Authors:  Pawel Górecki; Gordon J Burleigh; Oliver Eulenstein
Journal:  BMC Bioinformatics       Date:  2011-02-15       Impact factor: 3.169

5.  Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

Authors:  Pawel Górecki; Oliver Eulenstein
Journal:  BMC Bioinformatics       Date:  2012-06-25       Impact factor: 3.169

6.  Embedding gene trees into phylogenetic networks by conflict resolution algorithms.

Authors:  Marcin Wawerka; Dawid Dąbkowski; Natalia Rutecka; Agnieszka Mykowiecka; Paweł Górecki
Journal:  Algorithms Mol Biol       Date:  2022-05-19       Impact factor: 1.721

7.  Trichinella spiralis: Adaptation and parasitism.

Authors:  Dante Zarlenga; Zhengyuan Wang; Makedonka Mitreva
Journal:  Vet Parasitol       Date:  2016-07-02       Impact factor: 2.738

8.  The draft genome of the parasitic nematode Trichinella spiralis.

Authors:  Makedonka Mitreva; Douglas P Jasmer; Dante S Zarlenga; Zhengyuan Wang; Sahar Abubucker; John Martin; Christina M Taylor; Yong Yin; Lucinda Fulton; Pat Minx; Shiaw-Pyng Yang; Wesley C Warren; Robert S Fulton; Veena Bhonagiri; Xu Zhang; Kym Hallsworth-Pepin; Sandra W Clifton; James P McCarter; Judith Appleton; Elaine R Mardis; Richard K Wilson
Journal:  Nat Genet       Date:  2011-02-20       Impact factor: 38.330

9.  Exploring metazoan evolution through dynamic and holistic changes in protein families and domains.

Authors:  Zhengyuan Wang; Dante Zarlenga; John Martin; Sahar Abubucker; Makedonka Mitreva
Journal:  BMC Evol Biol       Date:  2012-08-03       Impact factor: 3.260

10.  Duplications and losses in gene families of rust pathogens highlight putative effectors.

Authors:  Amanda L Pendleton; Katherine E Smith; Nicolas Feau; Francis M Martin; Igor V Grigoriev; Richard Hamelin; C Dana Nelson; J Gordon Burleigh; John M Davis
Journal:  Front Plant Sci       Date:  2014-06-26       Impact factor: 5.753
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