Dr. Patrick Kück
Research interests
Molecular Systematic Approaches
Sequence Alignments
Algorithms and improvement of alignment and masking heuristics, string similarity and their role as first homology assessment, structure sequences and their influence on alignment quality, gap weights, alignment refinement techniques.
Algorithms and improvement of alignment and masking heuristics, string similarity and their role as first homology assessment, structure sequences and their influence on alignment quality, gap weights, alignment refinement techniques.
Tree Reconstructions
Evolutionary model parameter and their impact on phylogenetic trees, consistency and inconsistency of maximum likelihood calculations especially in terms of sensitivity towards different long branch effects, distance matrix methods, bayesian analysis, split decompositions, supermatrix and supertree approaches, bootstrap and permutation tests, microsatellite models.
Evolutionary model parameter and their impact on phylogenetic trees, consistency and inconsistency of maximum likelihood calculations especially in terms of sensitivity towards different long branch effects, distance matrix methods, bayesian analysis, split decompositions, supermatrix and supertree approaches, bootstrap and permutation tests, microsatellite models.
Algorithms
Deterministic algorithms that operate on strings and sequences like linear-time pattern matching algorithms (preprocessing methods), subtree pruning and regrafting, sublinear-time algorithms with widely used methods for biological database search Phylogenomic Phylogenetic signal improvement in gene as well as restriction super matrices, handling of expressed sequence tags (ESTs), mixed model analysis for phylogenomic purposes, concatenation processes, amplified fragment-length polymorphism (AFLP) analysis, sequence data base search and BLAST.
Deterministic algorithms that operate on strings and sequences like linear-time pattern matching algorithms (preprocessing methods), subtree pruning and regrafting, sublinear-time algorithms with widely used methods for biological database search Phylogenomic Phylogenetic signal improvement in gene as well as restriction super matrices, handling of expressed sequence tags (ESTs), mixed model analysis for phylogenomic purposes, concatenation processes, amplified fragment-length polymorphism (AFLP) analysis, sequence data base search and BLAST.
Perl Programming
Script Development
Data matrices as well as sequence alignments and tree reconstruction improvement, sequence concatenation, secondary structure inference, split decomposition and data base search, primer search, usage of bioperl modules.
Data matrices as well as sequence alignments and tree reconstruction improvement, sequence concatenation, secondary structure inference, split decomposition and data base search, primer search, usage of bioperl modules.
Pipeline Development
Design of simulation processes for alignment masking and tree algorithm tests, secondary structure and long branch estimates.
Design of simulation processes for alignment masking and tree algorithm tests, secondary structure and long branch estimates.
