190 related articles for article (PubMed ID: 35888084)
1. Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method.
Bremer N; Knopp M; Martin WF; Tria FDK
Life (Basel); 2022 Jul; 12(7):. PubMed ID: 35888084
[TBL] [Abstract][Full Text] [Related]
2. On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.
Kundu S; Bansal MS
BMC Bioinformatics; 2018 Aug; 19(Suppl 9):290. PubMed ID: 30367593
[TBL] [Abstract][Full Text] [Related]
3. Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.
Williams TA; Davín AA; Morel B; Szánthó LL; Spang A; Stamatakis A; Hugenholtz P; Szöllősi GJ
Genome Biol Evol; 2023 Jul; 15(7):. PubMed ID: 37463417
[TBL] [Abstract][Full Text] [Related]
4. Reconciliation and local gene tree rearrangement can be of mutual profit.
Nguyen TH; Ranwez V; Pointet S; Chifolleau AM; Doyon JP; Berry V
Algorithms Mol Biol; 2013 Apr; 8(1):12. PubMed ID: 23566548
[TBL] [Abstract][Full Text] [Related]
5. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.
Górecki P; Eulenstein O
BMC Bioinformatics; 2012 Jun; 13 Suppl 10(Suppl 10):S14. PubMed ID: 22759419
[TBL] [Abstract][Full Text] [Related]
6. Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
Kordi M; Bansal MS
IEEE/ACM Trans Comput Biol Bioinform; 2019; 16(4):1077-1090. PubMed ID: 28622673
[TBL] [Abstract][Full Text] [Related]
7. Efficient exploration of the space of reconciled gene trees.
Szöllõsi GJ; Rosikiewicz W; Boussau B; Tannier E; Daubin V
Syst Biol; 2013 Nov; 62(6):901-12. PubMed ID: 23925510
[TBL] [Abstract][Full Text] [Related]
8. Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.
Harris BJ; Sheridan PO; Davín AA; Gubry-Rangin C; Szöllősi GJ; Williams TA
Methods Mol Biol; 2022; 2569():189-211. PubMed ID: 36083449
[TBL] [Abstract][Full Text] [Related]
9. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.
Stolzer M; Lai H; Xu M; Sathaye D; Vernot B; Durand D
Bioinformatics; 2012 Sep; 28(18):i409-i415. PubMed ID: 22962460
[TBL] [Abstract][Full Text] [Related]
10. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.
Wu YC; Rasmussen MD; Bansal MS; Kellis M
Genome Res; 2014 Mar; 24(3):475-86. PubMed ID: 24310000
[TBL] [Abstract][Full Text] [Related]
11. Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations.
Chan YB; Ranwez V; Scornavacca C
J Theor Biol; 2017 Nov; 432():1-13. PubMed ID: 28801222
[TBL] [Abstract][Full Text] [Related]
12. Fast algorithm for the reconciliation of gene trees and LGT networks.
Scornavacca C; Mayol JCP; Cardona G
J Theor Biol; 2017 Apr; 418():129-137. PubMed ID: 28111320
[TBL] [Abstract][Full Text] [Related]
13. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods.
Nguyen TH; Ranwez V; Berry V; Scornavacca C
PLoS One; 2013; 8(10):e73667. PubMed ID: 24124449
[TBL] [Abstract][Full Text] [Related]
14. Reconciliation with non-binary species trees.
Vernot B; Stolzer M; Goldman A; Durand D
J Comput Biol; 2008 Oct; 15(8):981-1006. PubMed ID: 18808330
[TBL] [Abstract][Full Text] [Related]
15. Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae.
Ness RW; Graham SW; Barrett SC
Mol Biol Evol; 2011 Nov; 28(11):3009-18. PubMed ID: 21633114
[TBL] [Abstract][Full Text] [Related]
16. Gene tree correction for reconciliation and species tree inference.
Swenson KM; Doroftei A; El-Mabrouk N
Algorithms Mol Biol; 2012 Nov; 7(1):31. PubMed ID: 23167951
[TBL] [Abstract][Full Text] [Related]
17. Inferring phylogeny from whole genomes.
Górecki P; Tiuryn J
Bioinformatics; 2007 Jan; 23(2):e116-22. PubMed ID: 17237078
[TBL] [Abstract][Full Text] [Related]
18. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.
Szöllősi GJ; Davín AA; Tannier E; Daubin V; Boussau B
Philos Trans R Soc Lond B Biol Sci; 2015 Sep; 370(1678):20140335. PubMed ID: 26323765
[TBL] [Abstract][Full Text] [Related]
19. The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.
Gorecki P; Eulenstein O; Tiuryn J
IEEE/ACM Trans Comput Biol Bioinform; 2021; 18(6):2125-2135. PubMed ID: 31150345
[TBL] [Abstract][Full Text] [Related]
20. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution.
Hahn MW
Genome Biol; 2007; 8(7):R141. PubMed ID: 17634151
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
