The Leibniz Institute for the Analysis of Biodiversity Change

is a research museum of the Leibniz Association

Algorithmic Development

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Info

In preparation ....

Staff

Scientist, permanent position

Dr. Patrick Kück

Head of Section

Tel: +49 228 9122-404

Fax: +49 228 9122-212

E-Mail: P.Kueck [at] leibniz-lib.de

MSc or Diploma Candidate

Juliane Romahn

Tel: +49 228 9122-406

Fax: +49 228 9122-212

E-Mail: s6juroma [at] uni-bonn.de

Nathan Seidel

Tel: +49 228 9122-404

Fax: +49 228 9122-212

E-Mail: nseidel [at] uni-bonn.de

Projects

2019

APPETITE

APPETITE is a new automated process-pipeline for molecular phylogenetic purposes with nearly endless analytical possibilities. APPETITE

Project lead:

Dr. Patrick Kück

2018

Sherlock

Sherlock is an automated process pipeline for statistical evaluation of patristic tree-distance variation given partitioned or non-partitioned molecular sequence data.

Project lead:

Dr. Patrick Kück

2014

Countering Systematic Bias in Phylogenetics

PhyQuart, a new algorithm combining Hennigian logic and Maximum Likelihood estimation, represents a completely new strategy for the evaluation of molecular data based on a site pattern classification for quartets of aligned sequences.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig, European Union

2013

FASconCAT-G: extensive alignment preparations

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences and the generation of partitioned files for MrBayes and RAxML analyses.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

AliGROOVE – visualization of heterogeneous sequence divergence

AliGROOVE determines and visualizes the content of potentially randomized sequence similarities and alignment ambiguities in multiple sequence alignments.The AliGROOVE algorithm is an adaptation of the recently published ALISCORE masking algorithm (Misof & Misof, 2009, Kück et al., 2010). AliGROOVE summarizes site scores of profiles of sequence similarity normalized over the whole alignment length from each pairwise comparison and translates the obtained scoring distances between sequences into a similarity Matrix

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

BaCoCa – assessment of sequence biases

BaCoCa is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions.The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in Perl and works on WindowsPCs, Macs and Linux running systems.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2012

Identification of sources of error in molecular phylogenetic analyses

The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2011

Automated masking of AFLP markers

AMARE is designed to optimize the signal-to-noise ratio in AFLP data sets (single or multiple primer combinations). It identifies potentially erroneous AFLP genotyping errors as the number of non-reproducible scored markers between replicated AFLP profiles of single individuals. As a measure of overall data quality, it simultaneously estimates general replicate error rates.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2010

FASconCAT - convenient handling of data matrices

FASconCAT is a user-friendly software that concatenates rapidly different kinds of sequence data into one supermatrix file.

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

2009

ALISCORE - Masking of Multiple Sequence Alignments

Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies.

Project lead:

Prof. Dr. Bernhard Misof

Funding:

Zoological Research Museum Alexander Koenig

Publications

Published in

2022

Kück, P., Romahn, J., Meusemann, K. (2022): Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support. - NAR Genomics and Bioinformatics. Accepted.Ro

[read more]

Seidel, N.I., Geiger, M.F., Kück, P. (2022): SHERLOCK – an Automatized Analysis of Molecular Sequence Variation in Species Communities Using Statistical Tests on Patristic Tree Distances. - Biodiversity Online J. 2(4). BOJ. 00541.

[read more]

2017

Kück P, Wilkinson M, Gross C, Foster PG, Wägele JW (2017): Can quartet anal yses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data? PLoS ONE, 12(8):e0183393, doi:10.1371/journal. pone.0183393

[read more]

Links:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183393

2015

Kück P, Wägele JW (2015): Plesiomorphic character states cause systematic errors in molecular phylogenetic analyses: a simulation study. Cladistics, 0:1-18, doi:10.1111/cla.12132

[read more]

Links:

http://onlinelibrary.wiley.com/doi/10.1111/cla.12132/full

2014

Kück P, Struck T (2014): BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions. Mol. Phylogen. Evol. 70:94-98

[read more]

Links:

http://www.sciencedirect.com/science/article/pii/S1055790313003655?via%3Dihub

Misof B, Meusemann, K, vonReumont BM, Kück P, Prohaska SJ, Stadler, P (2014): A priori assessment of data quality in molecular phylogenetics. Algorithms Mol. Biol., 9:22

[read more]

Links:

https://almob.biomedcentral.com/articles/10.1186/s13015-014-0022-4

Struck T, Wey-Fabrizius AR, Golombeck A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, Kück P, Herlyn H, Hankeln T (2014): Platyzoan paraphyly based on phylogenomic data supports a non-coelomate ancestry of Spiralia. Mol. Biol. Evol. 31:1833-1849, doi:10.1093/molbev/msu143

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Links:

https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu143

Kück P, Longo GC (2014): FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool., 11:81

[read more]

Links:

https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-014-0081-x

2013

Misof B, Meyer B, von Reumont B, Kück P, Misof K, Meusemann K (2013): Selecting informative subsets of sparse supermatrices increases the chance to find correct trees. BMC Bioinformatics, 14:348

[read more]

Links:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-348

2012

Kück P, Greve, C, Misof B, Gimnich F (2012): Automated masking of AFLP markers improves reliability of phylogenetic analyses. PLoS ONE, 7(11):e49119. doi:10.1371/journal.pone.0049119

[read more]

Links:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049119

2011

Kück P, Hita Garcia F, Misof B, Meusemann K (2011): Improved phylogenetic analyses corroborate a plausible position of Martialis heureka in the Ant Tree of Life. PLoS ONE, 6(6):e21031. doi:10.1371/journal.pone.0021031

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Links:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021031

2010

Hita Garcia F, Fischer G, Kück P, Thormann B, Peters MK (2010) Tetramorium boehmei sp. n. – a new ant (Hymenoptera: Formicidae) species from the Kakamega Forest, Western Kenya. Bonn zoological Bulletin 57 (2): 359–366.

[read more]

Links:

http://zoologicalbulletin.de/BzB_Volumes/Volume_57_2/359_366_BzB57_2_Garcia_Francisco_Hita_et_al.PDF

Kück P, Meusemann K (2010): FASconCAT: Convenient handling of data matrices. Mol. Phylogen. Evol. 56:1115-1118

[read more]

Links:

https://www.deepdyve.com/lp/elsevier/fasconcat-convenient-handling-of-data-matrices-3FJNZSfEV4