Blog about science (biology), Linux (and its use in science, ...) and about another software, about school, scouting (mostly about ecological education), and photogallery. And sometimes more.

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.

Mallomonas alpestrina sp. nov. (Synurales, Chrysophyceae, Stramenopiles) and its spineless relatives—Mallomonas alata group

In this paper, we define the Mallomonas alata group and describe M. alpestrina sp. nov. from an oligotrophic high mountain glacial lake on the slopes of Haba Xue Shan (Haba Snow Mountain), China. The Mallomonas alata group is excluded from the M. pumilio group primarily based on the approximately triangular shape of the collar scales, the small hook-like protruded dome, and one considerably broader anterior flange of the body scale. We extend previous research on small species from the section Torquatae with reticulated scale-shield pattern.

Microsatellite variation, sexual reproduction and taxonomic revision of Taraxacum sect. Dioszegia: relationships at a large spatial scale

Tagy: 

Taraxacum serotinumThe coexistence of agamospermy and sexuality characterizes most of the ~60 sections of the genus Taraxacum. Section Dioszegia, comprising T. serotinum and its allies, are an exception because only sexuals are reported for all the members of this group. On the basis of the analysis of microsatellite (SSRs) variation, distribution and morphology, we addressed problems related to their mode of reproduction, among-population relationships, taxonomy and within-population variation, using samples from populations in an area extending from southern France to the European part of southern Russia and Iran.

PF 2015

Články: 

Pour féliciter 2015!

Course of work with molecular data in R 2015

Tagy: 

Since academic year 2015/16 is the course scheduled in SIS as MB120C16.

R is nowadays probably the most powerful tool for statistics of all types. There are plenty of modules available for work with molecular data. Those will be introduced during the course. Previous knowledge of R is useful, but not necessary. Course will be taught from January 14 to 16, 2015 from 9 AM to about 5 PM at the Department of Botany, Faculty of Science, Charles University in Prague in classroom "Krajinova posluchárna" (B14, 2nd mezzanine on the end of the corridor; Wednesday and Thursday) and in classroom "posluchárna OŽP" (B12, 1st mezzanine on the end of the corridor on right side; Friday).

Presentation with test data is available

Course of work in Linux command line not only for MetaCentrum 2015

Tagy: 

Since academic year 2015/16 is the course scheduled in SIS as MB120C17.

Don't be afraid of command line! It is friendly and powerful tool. Practically identical is command line also in Mac OS X, BSD and another UNIX-based systems, not only in Linux. Basic knowledge of Linux is not conditional. Course will be taught in Linux, but most of the point are applicable also for another UNIX systems like Mac OS X. Course will be taught January 26 and 27, 2015 from 9 AM to about 5 PM at the Department of Botany, Faculty of Science, Charles University in Prague in classroom "Praktikum OŽP" (B13, 1st mezzanine on the end of the corridor on left side).

Presentation with test data is available.

Structure, R and Linux

Tagy: 

Structure is very popular software for revealing population structure. Here I describe easy workflow how to run independent runs of Structure in parallel to speed up whole process using statistical software R and how to facilitate use of CLUMPP and distruct with easy BASH scripts. Of course, we work on Linux (although another UNIX systems like Mac OS X will be very similar).

Arlequin and R under Linux

Tagy: 

Arlequin is very popular tool for population genetics and in recent version (3.5) it has version running on Linux (arlecore, only computational core without GUI) as well as possibility to parse output using R statistical language. Those two features are described only briefly in official manual. I faced some issues when running Arlequin on Linux and parsing output using R.

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