---
_id: '2409'
abstract:
- lang: eng
text: "Background: The availability of many gene alignments with overlapping taxon
sets raises the question of which strategy is the best to infer species phylogenies
from multiple gene information. Methods and programs abound that use the gene
alignment in different ways to reconstruct the species tree. In particular, different
methods combine the original data at different points along the way from the underlying
sequences to the final tree. Accordingly, they are classified into superalignment,
supertree and medium-level approaches. Here, we present a simulation study to
compare different methods from each of these three approaches.\r\n\r\nResults:
We observe that superalignment methods usually outperform the other approaches
over a wide range of parameters including sparse data and gene-specific evolutionary
parameters. In the presence of high incongruency among gene trees, however, other
combination methods show better performance than the superalignment approach.
Surprisingly, some supertree and medium-level methods exhibit, on average, worse
results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions:
For some methods, using the reconstructed gene tree as an estimation of the species
tree is superior to the combination of incomplete information. Superalignment
usually performs best since it is less susceptible to stochastic error. Supertree
methods can outperform superalignment in the presence of gene-tree conflict."
acknowledgement: Financial support from the Wiener Wissenschafts-, Forschungs- and
Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from
the German Research Foundation (DFG, SPP-1174).
article_number: '37'
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Heiko
full_name: Schmidt, Heiko
last_name: Schmidt
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets . Algorithms for Molecular Biology.
2010;5(1). doi:10.1186/1748-7188-5-37
apa: Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny
reconstruction methods combining overlapping gene data sets . Algorithms for
Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37
chicago: Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny
Reconstruction Methods Combining Overlapping Gene Data Sets .” Algorithms for
Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.
ieee: A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets ,” Algorithms for Molecular Biology,
vol. 5, no. 1. BioMed Central, 2010.
ista: Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets . Algorithms for Molecular Biology.
5(1), 37.
mla: Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining
Overlapping Gene Data Sets .” Algorithms for Molecular Biology, vol. 5,
no. 1, 37, BioMed Central, 2010, doi:10.1186/1748-7188-5-37.
short: A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology
5 (2010).
date_created: 2018-12-11T11:57:30Z
date_published: 2010-12-06T00:00:00Z
date_updated: 2021-01-12T06:57:18Z
day: '06'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1748-7188-5-37
file:
- access_level: open_access
checksum: e2497285388bc4da629bafb46662eb43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:16Z
date_updated: 2020-07-14T12:45:40Z
file_id: '4739'
file_name: IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf
file_size: 723929
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Algorithms for Molecular Biology
publication_status: published
publisher: BioMed Central
publist_id: '4517'
pubrep_id: '939'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Accuracy of phylogeny reconstruction methods combining overlapping gene data
sets '
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2010'
...