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Bioinformatika

Od vojta , 26 Červenec, 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
Bioinformatika
Botanický ústav AV
Fylogenetika
HybSeq
Linux (a jiný software)
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
Od vojta , 25 Únor, 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
Bioinformatika
Botanický ústav AV
Fylogenetika
Fylogeografie
Linux (a jiný software)
Populační genetika
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
Od vojta , 29 Prosinec, 2020

Parallel Alpine Differentiation in Arabidopsis arenosa

Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested.

Články
Arabidopsis a Brassicaceae
Bioinformatika
Botanický ústav AV
Fylogenetika
Populační genetika
Věda, výzkum, biologie
Od vojta , 19 Prosinec, 2019

HybSeq course 2020

Intensive 4-days (5th day is not compulsory, but is open for any discussion, if there would be interest) course to learn all theory about HybSeq and practically learn how to analyze HybSeq data, how to solve all problems, and how to evaluate differences among gene trees. Important part is enough time to discuss everything, including practical problems and projects of individual participants.

Články
Bioinformatika
HybSeq
Linux (a jiný software)
Přírodovědecká fakulta UK
Věda, výzkum, biologie
Výuka
Od vojta , 2 Srpen, 2018

Hunting the treasure of Cape Oxalis diversity

Poster presented at Botany 2018 conference of the Botanical Society of America titled Hunting the treasure of Cape Oxalis diversity (Zeisek, Oberlander, Dreyer, Schmickl, Schneeweiss):

Články
Bioinformatika
Botanický ústav AV
Fylogenetika
HybSeq
Oxalis
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie
Od vojta , 26 Listopad, 2015

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in non-model organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region.

Články
Bioinformatika
Fylogenetika
HybSeq
Linux (a jiný software)
Oxalis
Přírodovědecká fakulta UK
Taxonomie
Věda, výzkum, biologie

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Bioinformatika
  • Czech Czech
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Proč používat Linux

openSUSE.org

Průvodce Linuxem

KDE - K Desktop Environment

openSUSE GNU/Linux

ORCID iD iconhttps://orcid.org/0000-0003-3481-9367

ResearchID/Publons

GitHub Logo, https://github.com/V-Z

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Licence Creative Commons

Dílo dílo, jehož autorem je Vojtěch Zeisek, podléhá licenci Creative Commons Uveďte původ-Neužívejte komerčně-Nezpracovávejte 4.0 Mezinárodní.

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