Vojtěch Zeisek - Per aspera, Asparagus et Aspergillus ad A/astra. https://trapa.cz/en en PF 2023 https://trapa.cz/pf2023 <span class="field field--name-title field--type-string field--label-hidden">PF 2023</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Pour féliciter 2023!</p> <p><img alt="PF 2023" data-entity-type="file" data-entity-uuid="b5d93392-6798-424c-bb97-62c93319dfb0" src="/sites/default/files/inline-images/pf_2023_vjtz.jpg" width="1600" height="1068" loading="lazy" /></p> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Sat, 12/31/2022 - 18:54</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/others" hreflang="en">Others</a></div> </div> </div> Sat, 31 Dec 2022 17:54:23 +0000 vojta 134 at https://trapa.cz Kurz práce s molekulárními daty v R 2023 https://trapa.cz/cs/kurz-molekularni-data-r-2023 <span class="field field--name-title field--type-string field--label-hidden"> Course of work with molecular data in R 2023</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><a href="https://www.r-project.org/">R</a> 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.</p> <p>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.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 10/12/2022 - 10:16</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/phylogeny" hreflang="en">Phylogeny</a></div> <div class="field__item"><a href="/en/phylogeo" hreflang="en">Phylogeography</a></div> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/popgen" hreflang="en">Population genetics</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/r" hreflang="en">R</a></div> <div class="field__item"><a href="/en/taxonomy" hreflang="en">Taxonomy</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Wed, 12 Oct 2022 08:16:00 +0000 vojta 133 at https://trapa.cz Kurz práce v příkazové řádce Linuxu nejen pro MetaCentrum 2023 https://trapa.cz/cs/kurz-prikazove-radky-linuxu-2023 <span class="field field--name-title field--type-string field--label-hidden">Course of work in Linux command line not only for MetaCentrum 2023</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 10/12/2022 - 10:07</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/opensuse" hreflang="en">openSUSE</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Wed, 12 Oct 2022 08:07:51 +0000 vojta 132 at https://trapa.cz The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae) https://trapa.cz/relationship-between-transposable-elements-and-eco-niches%20in-gcfr-pteronia <span class="field field--name-title field--type-string field--label-hidden">The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae)</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 10/12/2022 - 09:19</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/bioinformatics" hreflang="en">Bioinformatics</a></div> <div class="field__item"><a href="/en/ibot-cas" hreflang="en">Institute of Botany, Czech Academy of Sciences</a></div> <div class="field__item"><a href="/en/phylogeny" hreflang="en">Phylogeny</a></div> <div class="field__item"><a href="/en/hybseq" hreflang="en">HybSeq</a></div> <div class="field__item"><a href="/en/science" hreflang="en">Science, research, biology</a></div> </div> </div> Wed, 12 Oct 2022 07:19:20 +0000 vojta 131 at https://trapa.cz The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution https://trapa.cz/importance-considering-evo-hist-polyploids-climatic-niche-evo <span class="field field--name-title field--type-string field--label-hidden">The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Although whole-genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 10/12/2022 - 09:09</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/arabidopsis-brassicaceae" hreflang="en">Arabidopsis and Brassicaceae</a></div> <div class="field__item"><a href="/en/bioinformatics" hreflang="en">Bioinformatics</a></div> <div class="field__item"><a href="/en/ibot-cas" hreflang="en">Institute of Botany, Czech Academy of Sciences</a></div> <div class="field__item"><a href="/en/phylogeo" hreflang="en">Phylogeography</a></div> <div class="field__item"><a href="/en/popgen" hreflang="en">Population genetics</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/science" hreflang="en">Science, research, biology</a></div> </div> </div> Wed, 12 Oct 2022 07:09:04 +0000 vojta 130 at https://trapa.cz Target enrichment v rostlinné systematice aneb HybSeq kurz 2022 https://trapa.cz/cs/node/129 <span class="field field--name-title field--type-string field--label-hidden">Target enrichment for plant systematics - HybSeq course 2022</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 06/03/2022 - 11:42</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/bioinformatics" hreflang="en">Bioinformatics</a></div> <div class="field__item"><a href="/en/phylogeny" hreflang="en">Phylogeny</a></div> <div class="field__item"><a href="/en/hybseq" hreflang="en">HybSeq</a></div> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/science" hreflang="en">Science, research, biology</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Fri, 03 Jun 2022 09:42:46 +0000 vojta 129 at https://trapa.cz Virtual machine for my courses https://trapa.cz/vm-for-courses <span class="field field--name-title field--type-string field--label-hidden">Virtual machine for my courses</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>For my <a href="/en/teaching">courses</a> ofwork in Linux command line not only for MetaCentrum and with molecular data in R I provide VirtualBox image, which allows to run complete desktop Linux (in this case openSUSE Leap) with all preinstalled applications needed for both courses. It's easy way how to get fully working Linux to play with. It requires at least bit powerful notebook, e.g. at least quad-core with at least 8 GB RAM, but more is better.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Tue, 01/11/2022 - 16:37</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/bioinformatics" hreflang="en">Bioinformatics</a></div> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/opensuse" hreflang="en">openSUSE</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Tue, 11 Jan 2022 15:37:03 +0000 vojta 128 at https://trapa.cz Kurz práce s molekulárními daty v R 2022 https://trapa.cz/cs/kurz-molekularni-data-r-2022 <span class="field field--name-title field--type-string field--label-hidden"> Course of work with molecular data in R 2022</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><a href="https://www.r-project.org/">R</a> 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.</p> <p>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.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 11/11/2021 - 12:55</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/phylogeny" hreflang="en">Phylogeny</a></div> <div class="field__item"><a href="/en/phylogeo" hreflang="en">Phylogeography</a></div> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/popgen" hreflang="en">Population genetics</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/r" hreflang="en">R</a></div> <div class="field__item"><a href="/en/taxonomy" hreflang="en">Taxonomy</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Thu, 11 Nov 2021 11:55:10 +0000 vojta 126 at https://trapa.cz Kurz práce v příkazové řádce Linuxu nejen pro MetaCentrum 2022 https://trapa.cz/cs/kurz-prikazove-radky-linuxu-2022 <span class="field field--name-title field--type-string field--label-hidden">Course of work in Linux command line not only for MetaCentrum 2022</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 11/11/2021 - 11:51</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/opensuse" hreflang="en">openSUSE</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/teaching" hreflang="en">Teaching</a></div> </div> </div> Thu, 11 Nov 2021 10:51:01 +0000 vojta 125 at https://trapa.cz Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae https://trapa.cz/node/123 <span class="field field--name-title field--type-string field--label-hidden">Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>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 <em>Malus domestica</em> genome.</p></div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/en/user/1" typeof="schema:Person" property="schema:name" datatype="">vojta</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 07/26/2021 - 12:46</span> <div class="field field--name-taxonomy-vocabulary-2 field--type-entity-reference field--label-inline clearfix"> <div class="field__label">Články</div> <div class="field__items"> <div class="field__item"><a href="/en/bioinformatics" hreflang="en">Bioinformatics</a></div> <div class="field__item"><a href="/en/ibot-cas" hreflang="en">Institute of Botany, Czech Academy of Sciences</a></div> <div class="field__item"><a href="/en/phylogeny" hreflang="en">Phylogeny</a></div> <div class="field__item"><a href="/en/hybseq" hreflang="en">HybSeq</a></div> <div class="field__item"><a href="/en/linux" hreflang="en">Linux (and another software)</a></div> <div class="field__item"><a href="/en/natur-cuni" hreflang="en">Faculty of Science, Charles University</a></div> <div class="field__item"><a href="/en/taxonomy" hreflang="en">Taxonomy</a></div> <div class="field__item"><a href="/en/science" hreflang="en">Science, research, biology</a></div> </div> </div> Mon, 26 Jul 2021 10:46:46 +0000 vojta 123 at https://trapa.cz