How can I perform the analysis Bayesian skyline plots using BEAST?

More Cristian Cornejo Latorre's questions See All

How to calculate the taxonomic diversity of a community?

In particular I am interested in "the taxonomic distinctness measure". Is there any software where this analysis can be done? Best regarts Cristian

05 June 2017 8,535 2 View

How can the phylogenetic signal be measured or detected using mitochondrial DNA sequences?

I would like to know which software is the most commonly used or recommended for this analysis. Best regards, Cristian

02 March 2017 5,247 3 View

What is the size of the following Cyt b primers: MVZ11/MVZ28 MVZ05/MVZ08 MVZ21/MVZ16?

Greetings to all.Does anyone know the size (base pairs) of the following primers of the mitochondrial Cyt b gene? MVZ11/MVZ28MVZ05/MVZ08MVZ21/MVZ16 Best regards and thanks Cristian

11 December 2016 7,962 0 View

Hello everyone. For you, which are major evolutionary processes that can be assessed using mitochondrial DNA sequences?

I want have a better idea of the principal approaches that can be analyzed using mitochondrial DNA sequences in vertebrate evolutionary study.

09 October 2015 667 0 View

I would like know if you have a tutorial for using DIY ABC software or other similar programs about approximate Bayesian computation?

Hello everyone, I want to make an analysis using DNA mitochondrial sequences to further examine the history in some mammals populations in Mexico. Thanks and best regards, Cristian

08 September 2015 5,222 0 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

Are the apoptotic cells is positive for γH2AX ?

It has been documented that apoptotic cells themselves can induce phosphorylation of serine 139 on H2AX (γH2AX) due to DNA fragmentation during apoptosis (doi: 10.1074/jbc.275.13.9390). As γH2AX...

28 July 2024 7,983 2 View

Temim Deli

Dear Cristian

Please find attached a practical tutorial that can help you with performing BSP analysis, but you have to pay more attention with the different parameters needed for the analysis and that can differ according to the kind of data (i.e nucleotide substitution model, choice of prior distributions..). You have to fix them according to the nature of the analyzed sequences.

Good luck!

Cristian Cornejo Latorre

Dear Temim

Thank you very much for the information and practical tutorial, I will review in detail.

Best regards and thanks again

Cristian