Arjun Pal

13 Questions 4 Answers 0 Followers

Questions related from Arjun Pal

Does the presence of degenerate nucleotides in consensus sequences affect the results of population genetic analysis?

I want to run STRUCTURE on a nuclear gene of an insect species. The sequences that I have received are showing the presence of degenerate nucleotides in the consensus sequences. Do I need to edit...

01 March 2024 598 1 View

Why are there no bands in pcr inspite of DNA being present?

I am trying to extract DNA from a single insect from different sites. After extraction nanodrop readings show around 12-15 nanogram per microlitre concentration which is normal for the insect....

14 August 2023 5,153 4 View

How can I create a genotype profile from three nuclear markers?

I am trying to study the population genetic structure of a dipteran insect using three nuclear markers. One paper performed this by creating a genotype profile of each individual and then analysed...

03 February 2023 3,526 0 View

Can population structure analysis be performed using internal transcribed spacers instead of SSRs?

I am trying to determine the population structure of a dipteran insect. Most of the previous studies have performed the studies using SSRs. However I want to know if the same studies can be...

16 December 2022 8,572 1 View

How to interpret results for Mantel test performed in IBD?

I have performed a Mantel test using IBD software to test isolation by distance. However I am confused by the output of the software. Why there are so many analyses for a single dataset and which...

19 February 2022 2,450 3 View

Sequence submission Query in NCBI?

I am trying to submit COX1 sequence from a dipteran insect to NCBI. However I could sequence only a single strand (sequence using reverse primer). Can I submit the reverse sequence as it is or do...

07 October 2021 7,294 4 View

What is the significance of different values when calculating pairwise distance in MEGA-X?

I am calculating intraspecific pairwise distance for a species using p-distance and K2P model. The p-distance is showing highest distance within the species as 0.78 while K2P is showing the...

04 July 2021 5,981 1 View

Does remaining salt during DNA extraction carry over to sequencing after PCR and purification of PCR product?

We forgot a washing step during DNA extraction with 70% ethanol but washed it with 100% ethanol which was the next step, however PCR gave good bands at the expected size range. Will this salt...

13 June 2021 220 4 View

Why is pairwise alignment and BLAST search of two same sequences giving different percent identity?

Two seqences are being shown to be 100% similar in BLAST search but performing pairwise alignment via the EMBL server is showing the sequences to be around 46% similar. Why this difference in...

30 May 2021 3,446 4 View

I cannot seem to understand the error that Modeltest2 v2.1.4 is showing. Can someone help?

I want to use ModelTest2 for identifying optimal model of nucleotide substitution but it shows an error when the GUI is launched WARNING: PhyML binary is not in the list of compatibility:...

29 March 2021 8,984 2 View

How do I make a user tree file in Newick format for inferring ancestral sequences?

I am trying to infer ancestral sequences in MEGA X but the program is asking for a user tree file in Newick format. How do I create a user tree file in Newick format and what is the input file...

27 March 2021 9,470 3 View

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

01 March 2021 4,285 3 View

Is it possible to perform chi-squared test on continuous data?

Can I perform chi-squared test on continuous data? What changes if any do I have to make to the data to perform chi-squared test?

26 January 2021 4,152 9 View