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Taxonomy

By vojta , 9 September 2024

Course of work with molecular data in R 2025

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 17 October 2023

Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates

The first species-level phylogeny of the Sabulina verna group is presented. Genetic clusters are congruent with geography and mostly supported by morphological traits. Metalliferous and serpentine soils were colonized multiple times independently.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
Population genetics
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 27 September 2023

Course of work with molecular data in R 2024

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 21 June 2023

Phylogenetic challenges in a recently diversified and polyploid-rich Alyssum (Brassicaceae) lineage: low divergence, reticulation, and parallel polyploid speciation

Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events.

Články
Arabidopsis and Brassicaceae
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
HybSeq
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 12 October 2022

Course of work with molecular data in R 2023

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 11 November 2021

Course of work with molecular data in R 2022

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 26 July 2021

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 25 February 2021

STRUCTURE multi PBS Pro scripts

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.

Články
Bioinformatics
Institute of Botany, Czech Academy of Sciences
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
Taxonomy
Science, research, biology
By vojta , 6 October 2020

Course of work with molecular data in R 2021

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more.

Previous knowledge of R is useful, but not necessary. At least basic knowledge of molecular biology is required, previous knowledge about any methods how to analyse DNA data is recommended.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 6 March 2020

Course of work with molecular data in R 2020 in České Budějovice

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course. The course will be taught from October 19th to Friday 23rd (see below). The course will be exclusively on-line, there will be no personal meeting.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching

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