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References from Host-symbiont-gene phylogenetic reconciliation. Local targets link to admitted publications; unresolved targets remain external evidence.
How old are bacterial pathogens?
10.1098/rspb.2016.0990 · 2016 · External reference
Recombination and clonal groupings within Helicobacter pylori from different geographical regions
10.1046/j.1365-2958.1999.01382.x · 1999 · External reference
Disentangling host–microbiota complexity through hologenomics
10.1038/s41576-021-00421-0 · 2021 · External reference
Gene tree and species tree reconciliation with endosymbiotic gene transfer
10.1093/bioinformatics/btab328 · 2021 · External reference
How Long Does Wolbachia Remain on Board?
10.1093/molbev/msx073 · 2017 · External reference
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
10.1093/bioinformatics/bts225 · 2012 · External reference
Detecting Highways of Horizontal Gene Transfer
10.1089/cmb.2011.0066 · 2011 · External reference
Improved gene tree error correction in the presence of horizontal gene transfer
10.1093/bioinformatics/btu806 · 2015 · External reference
Reconciling Gene trees with Species Trees
2020 · External reference
Event-Based Cophylogenetic Comparative Analysis
10.1007/978-3-662-43550-2_20 · 2014 · External reference
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers
10.1101/127548 · 2017 · External reference
Rapid evolutionary innovation during an Archaean genetic expansion
10.1038/nature09649 · 2010 · External reference
Gene transfers can date the tree of life
10.1038/s41559-018-0525-3 · 2018 · External reference
EUCALYPT: efficient tree reconciliation enumerator
10.1186/s13015-014-0031-3 · 2015 · External reference
Models, algorithms and programs for phylogeny reconciliation
10.1093/bib/bbr045 · 2011 · External reference
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
10.1093/gbe/evx069 · 2017 · External reference
Reconstruction of an ancestral Yersinia pestisgenome and comparison with an ancient sequence
10.1186/1471-2164-16-s10-s9 · 2015 · External reference
RecPhyloXML: a format for reconciled gene trees
10.1093/bioinformatics/bty389 · 2018 · External reference
Unresolved reference
2003 · External reference
Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life
10.1098/rstb.2009.0033 · 2009 · External reference
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony
10.1093/bioinformatics/btw105 · 2016 · External reference
Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications
10.12688/wellcomeopenres.14826.1 · 2018 · External reference
Reconciling molecular evolution and evolutionary ecology studies: a phylogenetic reconciliation method for gene-symbiont-host systems
10.24072/pci.evolbiol.100593 · 2023 · External reference
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation
10.1145/3307339.3342168 · 2019 · External reference
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution
10.1093/bioinformatics/btz081 · 2019 · External reference
An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem
10.1145/3233547.3233603 · 2018 · External reference
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution
10.1109/tcbb.2018.2846253 · 2019 · External reference
Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model
10.1007/978-3-030-20242-2_7 · 2019 · External reference
Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems
10.1038/s41396-019-0533-6 · 2019 · External reference
Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees
10.1093/cz/zow018 · 2016 · External reference
The history of Helicobacter pylori : from phylogeography to paleomicrobiology
10.1016/j.cmi.2016.07.013 · 2016 · External reference
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity
10.1186/s12859-018-2164-8 · 2018 · External reference
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life
10.1093/nar/gkz246 · 2019 · External reference
Phylogenetic reconciliation
10.1371/journal.pcbi.1010621 · 2022 · External reference
Host symbiont gene reconciliation supple- mentary material [Data set]
10.5281/zenodo.7667342 · 2023 · External reference
GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss
10.1093/molbev/msaa141 · 2020 · External reference
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss
10.1093/molbev/msab365 · 2022 · External reference
Species tree-aware simultaneous reconstruction of gene and domain evolution
10.1101/336453 · 2018 · External reference
Inferring time-consistent and well-supported horizontal gene transfers
10.1109/bibm.2018.8621558 · 2018 · External reference
Defensive Bacteriome Symbiont with a Drastically Reduced Genome
10.1016/j.cub.2013.06.027 · 2013 · External reference
Computational approaches to species phylogeny inference and gene tree reconciliation
10.1016/j.tree.2013.09.004 · 2013 · External reference
Evolutionary origin of insect–Wolbachia nutritional mutualism
10.1073/pnas.1409284111 · 2014 · External reference
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
10.1093/bioinformatics/btac062 · 2022 · External reference
Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii
10.1371/journal.pgen.1003012 · 2012 · External reference
Unified modeling of gene duplication, loss, and coalescence using a locus tree
10.1101/gr.123901.111 · 2012 · External reference
Inferring Horizontal Gene Transfer
10.1371/journal.pcbi.1004095 · 2015 · External reference
A likelihood framework for inferring the evolution of geographic range on phylogenetic trees
10.1111/j.0014-3820.2005.tb00940.x · 2005 · External reference
Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis
10.1080/10635150701883881 · 2008 · External reference
Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography
10.1093/sysbio/46.1.195 · 1997 · External reference
eMPRess: a systematic cophylogeny reconciliation tool
10.1093/bioinformatics/btaa978 · 2020 · External reference
10.1093/oso/9780195088205.001.0001
10.1093/oso/9780195088205.001.0001 · 1994 · External reference
A Bayesian Method for Analyzing Lateral Gene Transfer
10.1093/sysbio/syu007 · 2014 · External reference
Vulnerability of the industrialized microbiota
10.1126/science.aaw9255 · 2019 · External reference
Event inference in multidomain families with phylogenetic reconciliation
10.1186/1471-2105-16-s14-s8 · 2015 · External reference
Lateral Gene Transfer from the Dead
10.1093/sysbio/syt003 · 2013 · External reference
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
10.1073/pnas.1202997109 · 2012 · External reference
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi
10.1098/rstb.2014.0335 · 2015 · External reference
Efficient Exploration of the Space of Reconciled Gene Trees
10.1093/sysbio/syt054 · 2013 · External reference
The Inference of Gene Trees with Species Trees
10.1093/sysbio/syu048 · 2014 · External reference
Ghost lineages can invalidate or even reverse findings regarding gene flow
10.1371/journal.pbio.3001776 · 2022 · External reference
The Story of Helicobacter pylori: Depicting Human Migrations from the Phylogeography
10.1007/5584_2019_356 · 2019 · External reference
Cophylogenetic Reconciliation with ILP
10.1109/tcbb.2015.2430336 · 2015 · External reference
Hosts, parasites, and horizontal gene transfer
10.1016/j.pt.2013.05.001 · 2013 · External reference
10.1093/acprof:oso/9780198567028.001.0001
10.1093/acprof:oso/9780198567028.001.0001 · 2006 · External reference
Cladogenesis, coalescence and the evolution of the three domains of life
10.1016/j.tig.2004.02.004 · 2004 · External reference
