---
_id: '2042'
abstract:
- lang: eng
text: 'Background: CRISPR is a microbial immune system likely to be involved in
host-parasite coevolution. It functions using target sequences encoded by the
bacterial genome, which interfere with invading nucleic acids using a homology-dependent
system. The system also requires protospacer associated motifs (PAMs), short motifs
close to the target sequence that are required for interference in CRISPR types
I and II. Here, we investigate whether PAMs are depleted in phage genomes due
to selection pressure to escape recognition.Results: To this end, we analyzed
two data sets. Phages infecting all bacterial hosts were analyzed first, followed
by a detailed analysis of phages infecting the genus Streptococcus, where PAMs
are best understood. We use two different measures of motif underrepresentation
that control for codon bias and the frequency of submotifs. We compare phages
infecting species with a particular CRISPR type to those infecting species without
that type. Since only known PAMs were investigated, the analysis is restricted
to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found
evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR
type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus
thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions:
The observed motif depletion in phages with hosts having CRISPR can be attributed
to selection rather than to mutational bias, as mutational bias should affect
the phages of all hosts. This observation implies that the CRISPR system has been
efficient in the groups discussed here.'
article_number: '663'
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with
CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663
apa: Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages
infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663
chicago: Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages
Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014.
https://doi.org/10.1186/1471-2164-15-663.
ieee: A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting
hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central,
2014.
ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting
hosts with CRISPR systems. BMC Genomics. 15(1), 663.
mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages
Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663,
BioMed Central, 2014, doi:10.1186/1471-2164-15-663.
short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:23Z
date_published: 2014-08-08T00:00:00Z
date_updated: 2025-09-29T11:52:17Z
day: '08'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1186/1471-2164-15-663
external_id:
isi:
- '000341528300001'
file:
- access_level: open_access
checksum: 3f6d2776b90a842a28359cc957d3d04b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:24Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4878'
file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf
file_size: 1489769
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '08'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_status: published
publisher: BioMed Central
publist_id: '5009'
pubrep_id: '396'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Motif depletion in bacteriophages infecting hosts with CRISPR systems
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2014'
...
---
_id: '2410'
abstract:
- lang: eng
text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis,
isolated from soil in Austria. It is the first phage to be discovered that infects
this species. Here, we present the complete genome sequence of this podovirus. '
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Gertraud
full_name: Stift, Gertraud
id: 2DB195CA-F248-11E8-B48F-1D18A9856A87
last_name: Stift
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence
of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements.
2013;1(3). doi:10.1128/genomeA.00216-13
apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013).
Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis.
Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13
chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan
P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus
Weihenstephanensis.” Genome Announcements. American Society for Microbiology,
2013. https://doi.org/10.1128/genomeA.00216-13.
ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete
genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,”
Genome Announcements, vol. 1, no. 3. American Society for Microbiology,
2013.
ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome
sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome
Announcements. 1(3).
mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel
Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements,
vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.
short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements
1 (2013).
corr_author: '1'
date_created: 2018-12-11T11:57:30Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2024-10-09T20:55:15Z
day: '13'
ddc:
- '576'
department:
- _id: JoBo
- _id: LifeSc
doi: 10.1128/genomeA.00216-13
file:
- access_level: open_access
checksum: 0751ec74b695567e0cdf02aaf9c26829
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:36Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5291'
file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf
file_size: 130026
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Genome Announcements
publication_status: published
publisher: American Society for Microbiology
publist_id: '4516'
pubrep_id: '398'
quality_controlled: '1'
scopus_import: 1
status: public
title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '2412'
abstract:
- lang: eng
text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable
immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer
sequences. Each spacer can provide specific immunity to invasive elements that
carry the same or a similar sequence. Even in closely related strains, spacer
content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot
be applied to quantify its rate of change since processes other than single nucleotide
changes determine its evolution.Methods We present probabilistic models that are
specific for spacer content evolution. They account for the different processes
of insertion and deletion. Insertions can be constrained to occur on one end only
or are allowed to occur throughout the array. One deletion event can affect one
spacer or a whole fragment of adjacent spacers. Parameters of the underlying models
are estimated for a pair of arrays by maximum likelihood using explicit ancestor
enumeration.Results Simulations show that parameters are well estimated on average
under the models presented here. There is a bias in the rate estimation when including
fragment deletions. The models also estimate times between pairs of strains. But
with increasing time, spacer overlap goes to zero, and thus there is an upper
bound on the distance that can be estimated. Spacer content similarities are displayed
in a distance based phylogeny using the estimated times.We use the presented models
to analyze different Yersinia pestis data sets and find that the results among
them are largely congruent. The models also capture the variation in diversity
of spacers among the data sets. A comparison of spacer-based phylogenies and Cas
gene phylogenies shows that they resolve very different time scales for this data
set.Conclusions The simulations and data analyses show that the presented models
are useful for quantifying spacer content evolution and for displaying spacer
content similarities of closely related strains in a phylogeny. This allows for
comparisons of different CRISPR arrays or for comparisons between CRISPR arrays
and nucleotide substitution rates.'
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution
. BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54
apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR
spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54
chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR
Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013.
https://doi.org/10.1186/1471-2148-13-54.
ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content
evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central,
pp. 54–54, 2013.
ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content
evolution . BMC Evolutionary Biology. 13(1), 54–54.
mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer
Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central,
2013, pp. 54–54, doi:10.1186/1471-2148-13-54.
short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.
corr_author: '1'
date_created: 2018-12-11T11:57:31Z
date_published: 2013-02-26T00:00:00Z
date_updated: 2025-09-29T14:15:59Z
day: '26'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-54
external_id:
isi:
- '000321524500001'
file:
- access_level: open_access
checksum: 029c7e0b198c19312b66ecce3cabb22f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:15Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5268'
file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf
file_size: 518729
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 54 - 54
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '4514'
pubrep_id: '397'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Probabilistic models for CRISPR spacer content evolution '
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2013'
...
---
_id: '2411'
abstract:
- lang: eng
text: The kingdom of fungi provides model organisms for biotechnology, cell biology,
genetics, and life sciences in general. Only when their phylogenetic relationships
are stably resolved, can individual results from fungal research be integrated
into a holistic picture of biology. However, and despite recent progress, many
deep relationships within the fungi remain unclear. Here, we present the first
phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion
to strengthen phylogenetic conclusions. We reason that branches (splits) recovered
with independent data and different tree reconstruction methods are likely to
reflect true evolutionary relationships. Two complementary phylogenomic data sets
based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed
with four different tree reconstruction methods shed light from different angles
on the fungal tree of life. Eleven additional data sets address specifically the
phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes,
respectively. The combined evidence from the resulting trees supports the deep-level
stability of the fungal groups toward a comprehensive natural system of the fungi.
In addition, our analysis reveals methodologically interesting aspects. Enrichment
for EST encoded data-a common practice in phylogenomic analyses-introduces a strong
bias toward slowly evolving and functionally correlated genes. Consequently, the
generalization of phylogenomic data sets as collections of randomly selected genes
cannot be taken for granted. A thorough characterization of the data to assess
possible influences on the tree reconstruction should therefore become a standard
in phylogenomic analyses.
article_processing_charge: No
author:
- first_name: Ingo
full_name: Ebersberger, Ingo
last_name: Ebersberger
- first_name: Ricardo
full_name: De Matos Simoes, Ricardo
last_name: De Matos Simoes
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Matthias
full_name: Gube, Matthias
last_name: Gube
- first_name: Erika
full_name: Kothe, Erika
last_name: Kothe
- first_name: Kerstin
full_name: Voigt, Kerstin
last_name: Voigt
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic
backbone for the fungi. Molecular Biology and Evolution. 2012;29(5):1319-1334.
doi:10.1093/molbev/msr285
apa: Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt,
K., & Von Haeseler, A. (2012). A consistent phylogenetic backbone for the
fungi. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msr285
chicago: Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube,
Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic
Backbone for the Fungi.” Molecular Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/molbev/msr285.
ieee: I. Ebersberger et al., “A consistent phylogenetic backbone for the
fungi,” Molecular Biology and Evolution, vol. 29, no. 5. Oxford University
Press, pp. 1319–1334, 2012.
ista: Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von
Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular
Biology and Evolution. 29(5), 1319–1334.
mla: Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.”
Molecular Biology and Evolution, vol. 29, no. 5, Oxford University Press,
2012, pp. 1319–34, doi:10.1093/molbev/msr285.
short: I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt,
A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.
date_created: 2018-12-11T11:57:30Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2025-09-30T08:21:34Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: JoBo
doi: 10.1093/molbev/msr285
external_id:
isi:
- '000303603300004'
file:
- access_level: open_access
checksum: d565dcac27d1736c0c378ea6fcf22d69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:30Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5013'
file_name: IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf
file_size: 754922
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 1319 - 1334
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '4515'
pubrep_id: '384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A consistent phylogenetic backbone for the fungi
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 29
year: '2012'
...
---
_id: '3370'
abstract:
- lang: eng
text: Supertree methods are widely applied and give rise to new conclusions about
phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for
supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have
been studied in greater detail, examples include shape bias (Wilkinson et al.
2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at
two matrix representation methods, matrix representation with compatibility (MRC)
and matrix representation with parsimony (MRP). Different null models of random
data are studied and the resulting tree shapes are investigated. Thereby I consider
unrooted trees and a bias in tree shape is determined by a tree balance measure.
The measure for unrooted trees is a modification of a tree balance measure for
rooted trees. I observe that depending on the underlying null model of random
data, the methods may resolve conflict in favor of more balanced tree shapes.
The analyses refer only to trees with the same taxon set, also known as the consensus
setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions
on how to deal with missing data.
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
citation:
ama: Kupczok A. Consequences of different null models on the tree shape bias of
supertree methods. Systematic Biology. 2011;60(2):218-225. doi:10.1093/sysbio/syq086
apa: Kupczok, A. (2011). Consequences of different null models on the tree shape
bias of supertree methods. Systematic Biology. Oxford University Press.
https://doi.org/10.1093/sysbio/syq086
chicago: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape
Bias of Supertree Methods.” Systematic Biology. Oxford University Press,
2011. https://doi.org/10.1093/sysbio/syq086.
ieee: A. Kupczok, “Consequences of different null models on the tree shape bias
of supertree methods,” Systematic Biology, vol. 60, no. 2. Oxford University
Press, pp. 218–225, 2011.
ista: Kupczok A. 2011. Consequences of different null models on the tree shape bias
of supertree methods. Systematic Biology. 60(2), 218–225.
mla: Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias
of Supertree Methods.” Systematic Biology, vol. 60, no. 2, Oxford University
Press, 2011, pp. 218–25, doi:10.1093/sysbio/syq086.
short: A. Kupczok, Systematic Biology 60 (2011) 218–225.
corr_author: '1'
date_created: 2018-12-11T12:02:57Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2025-09-30T08:59:18Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/sysbio/syq086
external_id:
isi:
- '000287255100009'
intvolume: ' 60'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.cs.univie.ac.at/3226/
month: '03'
oa: 1
oa_version: Submitted Version
page: 218 - 225
publication: Systematic Biology
publication_status: published
publisher: Oxford University Press
publist_id: '3241'
quality_controlled: '1'
status: public
title: Consequences of different null models on the tree shape bias of supertree methods
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 60
year: '2011'
...
---
_id: '3387'
abstract:
- lang: eng
text: 'Background: Supertree methods combine overlapping input trees into a larger
supertree. Here, I consider split-based supertree methods that first extract the
split information of the input trees and subsequently combine this split information
into a phylogeny. Well known split-based supertree methods are matrix representation
with parsimony and matrix representation with compatibility. Combining input trees
on the same taxon set, as in the consensus setting, is a well-studied task and
it is thus desirable to generalize consensus methods to supertree methods. Results:
Here, three variants of majority-rule (MR) supertrees that generalize majority-rule
consensus trees are investigated. I provide simple formulas for computing the
respective score for bifurcating input- and supertrees. These score computations,
together with a heuristic tree search minmizing the scores, were implemented in
the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/
plumist. The different MR methods were tested by simulation and on real data sets.
The search heuristic was successful in combining compatible input trees. When
combining incompatible input trees, especially one variant, MR(-) supertrees,
performed well. Conclusions: The presented framework allows for an efficient score
computation of three majority-rule supertree variants and input trees. I combined
the score computation with a heuristic search over the supertree space. The implementation
was tested by simulation and on real data sets and showed promising results. Especially
the MR(-) variant seems to be a reasonable score for supertree reconstruction.
Generalizing these computations to multifurcating trees is an open problem, which
may be tackled using this framework.'
article_number: '205'
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
citation:
ama: Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary
Biology. 2011;11(205). doi:10.1186/1471-2148-11-205
apa: Kupczok, A. (2011). Split based computation of majority rule supertrees. BMC
Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-205
chicago: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC
Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-205.
ieee: A. Kupczok, “Split based computation of majority rule supertrees,” BMC
Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011.
ista: Kupczok A. 2011. Split based computation of majority rule supertrees. BMC
Evolutionary Biology. 11(205), 205.
mla: Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC
Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205.
short: A. Kupczok, BMC Evolutionary Biology 11 (2011).
corr_author: '1'
date_created: 2018-12-11T12:03:03Z
date_published: 2011-07-13T00:00:00Z
date_updated: 2025-09-30T08:45:48Z
day: '13'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-11-205
external_id:
isi:
- '000294663400001'
file:
- access_level: open_access
checksum: 68da8d04af1b97b4cbe8606e2f92ddd8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:09Z
date_updated: 2020-07-14T12:46:11Z
file_id: '5058'
file_name: IST-2015-372-v1+1_1471-2148-11-205.pdf
file_size: 465042
relation: main_file
file_date_updated: 2020-07-14T12:46:11Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '205'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '3219'
pubrep_id: '372'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Split based computation of majority rule supertrees
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2011'
...
---
_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'
article_processing_charge: No
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: 2025-09-30T09:48:29Z
day: '06'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1748-7188-5-37
external_id:
isi:
- '000286183400001'
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'
isi: 1
issue: '1'
language:
- iso: eng
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2010'
...
---
_id: '3768'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Von Haeseler A. Comment on “A congruence index for testing topological
similarity between trees.” Bioinformatics. 2009;25(1):147-149. doi:10.1093/bioinformatics/btn539
apa: Kupczok, A., & Von Haeseler, A. (2009). Comment on “A congruence index
for testing topological similarity between trees.” Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btn539
chicago: Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘A Congruence Index
for Testing Topological Similarity between Trees.’” Bioinformatics. Oxford
University Press, 2009. https://doi.org/10.1093/bioinformatics/btn539.
ieee: A. Kupczok and A. Von Haeseler, “Comment on ‘A congruence index for testing
topological similarity between trees,’” Bioinformatics, vol. 25, no. 1.
Oxford University Press, pp. 147–149, 2009.
ista: Kupczok A, Von Haeseler A. 2009. Comment on ‘A congruence index for testing
topological similarity between trees’. Bioinformatics. 25(1), 147–149.
mla: Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘A Congruence Index for
Testing Topological Similarity between Trees.’” Bioinformatics, vol. 25,
no. 1, Oxford University Press, 2009, pp. 147–49, doi:10.1093/bioinformatics/btn539.
short: A. Kupczok, A. Von Haeseler, Bioinformatics 25 (2009) 147–149.
date_created: 2018-12-11T12:05:04Z
date_published: 2009-10-14T00:00:00Z
date_updated: 2025-07-02T06:49:41Z
day: '14'
doi: 10.1093/bioinformatics/btn539
extern: '1'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 147 - 149
publication: Bioinformatics
publication_status: published
publisher: Oxford University Press
publist_id: '2459'
status: public
title: Comment on 'A congruence index for testing topological similarity between trees'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2009'
...
---
_id: '3769'
abstract:
- lang: eng
text: The geometrical representation of the space of phylogenetic trees implies
a metric on the space of weighted trees. This metric, the geodesic distance, is
the length of the shortest path through that space. We present an exact algorithm
to compute this metric. For biologically reasonable trees, the implementation
allows fast computations of the geodesic distance, although the running time of
the algorithm is worst-case exponential. The algorithm was applied to pairs of
118 gene trees of the metazoa. The results show that a special path in tree space,
the cone path, which can be computed in linear time, is a good approximation of
the geodesic distance. The program GeoMeTree is a python implementation of the
geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree.
acknowledgement: 10.1089/cmb.2008.0068
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Arndt
full_name: von Haeseler,Arndt
last_name: Von Haeseler
- first_name: Steffen
full_name: Klaere,Steffen
last_name: Klaere
citation:
ama: Kupczok A, Von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance
between Phylogenetic Trees. Journal of Computational Biology. 2008;15(6):577-591.
doi:4200
apa: Kupczok, A., Von Haeseler, A., & Klaere, S. (2008). An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees. Journal of Computational
Biology. Mary Ann Liebert. https://doi.org/4200
chicago: Kupczok, Anne, Arndt Von Haeseler, and Steffen Klaere. “An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees.” Journal of Computational
Biology. Mary Ann Liebert, 2008. https://doi.org/4200.
ieee: A. Kupczok, A. Von Haeseler, and S. Klaere, “An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees.,” Journal of Computational Biology,
vol. 15, no. 6. Mary Ann Liebert, pp. 577–591, 2008.
ista: Kupczok A, Von Haeseler A, Klaere S. 2008. An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees. Journal of Computational Biology. 15(6),
577–591.
mla: Kupczok, Anne, et al. “An Exact Algorithm for the Geodesic Distance between
Phylogenetic Trees.” Journal of Computational Biology, vol. 15, no. 6,
Mary Ann Liebert, 2008, pp. 577–91, doi:4200.
short: A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology
15 (2008) 577–591.
date_created: 2018-12-11T12:05:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:04Z
day: '01'
doi: '4200'
extern: 1
intvolume: ' 15'
issue: '6'
month: '01'
page: 577 - 591
publication: Journal of Computational Biology
publication_status: published
publisher: Mary Ann Liebert
publist_id: '2458'
quality_controlled: 0
status: public
title: An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.
type: journal_article
volume: 15
year: '2008'
...
---
_id: '3767'
abstract:
- lang: eng
text: Models of RNA secondary structure folding are widely used to study evolution
in theory and simulation. However, systematic studies of the parameters involved
are rare. In this paper, we study by simulation how RNA evolution is influenced
by three different factors, namely the mutation rate, scaling of the fitness function,
and distance measure. We found that for low mutation rates the qualitative evolutionary
behavior is robust with respect to the scaling of the fitness function. For efficient
mutation rates, which are close to the error threshold, scaling and distance measure
have a strong influence on the evolutionary behavior. A global distance measure
that takes sequence information additively into account lowers the error threshold.
When using a local sequence-structure alignment for the distance, we observed
a smoother evolution of the fitness over time. Finally, in addition to the well
known error threshold, we identify another threshold of the mutation rate, called
divergence threshold, where the qualitative transient behavior changes from a
localized to an exploratory search.
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Peter
full_name: Dittrich,Peter
last_name: Dittrich
citation:
ama: Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019
apa: Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019
chicago: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019.
ieee: A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal
of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006.
ista: Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal
of Theoretical Biology. 238(3), 726–35.
mla: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.”
Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35,
doi:10.1016/j.jtbi.2005.06.019.
short: A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35.
date_created: 2018-12-11T12:05:03Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:03Z
day: '01'
doi: 10.1016/j.jtbi.2005.06.019
extern: 1
intvolume: ' 238'
issue: '3'
month: '01'
page: 726 - 35
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2461'
quality_controlled: 0
status: public
title: Determinants of simulated RNA evolution.
type: journal_article
volume: 238
year: '2006'
...