Ahasan Habib

10 Questions 37 Answers 0 Followers

Questions related from Ahasan Habib

Why General Time Reversible (GTR) model (Nei & Kumar 2000)?

Maximum-likelihood (ML) tree based on GTR, why we choose this GTR mode to construct a phylogenetic tree? Could anybody explain it with ref/article if there is any? I may find answer in Nei and...

03 April 2016 5,935 9 View

Can you help me with a DNA sequence alignment?

Hi, after aligning DNA sequences (generally I do it with BioEdit or MAFFT), what should I do with dot like "-----", should I just removed from both end and from middle? My amplified BP is 426 for...

05 April 2015 9,637 12 View

How can one trim primer sequences?

Hi, is there any software to trim off primer sequence from sequence (full length sequence). Is it possible to do so using BioEdit? or is there any software to find/place primer sequence and trim...

06 October 2014 939 2 View

Can anyone help with a problem in Arlequin performing?

I have been trying many times to perform Arlequin but following error message showing.. #[ERROR # 5] : haplotype already defined #[ERROR # 6] : unable to read sample data So where might be...

25 April 2014 3,771 5 View

Can anyone help me and send an example or sample file to run the Mantel test in Arlequin?

I have been trying and did set data as well, but Arlequin shows error/warning message. I am using mtDNA D-loop marker.

19 March 2014 9,022 2 View

Is there any free software to make a haplotype network or a haplotype spanning network from DNA sequence data?

Also, how can you convert a fasta format file to rdf? Thanks.

27 February 2014 346 40 View

DNA sequence phylogenetic tree?

I would like to take a DNA sequence from NCBI database with my samples' sequence as an outgroup to make a phylogenetic tree. so in this case, do I need to do alignment and eliminate that sequence...

06 February 2014 8,374 19 View

Do you have any idea of how to use/infer from 3 different markers at the same time?

To be more clear, I have 3 different markers that are all mtDNA (D-loop, cytb and 12s rRNA). I used them for the same fish species and want to analyze them all together. If you have any papers on...

15 December 2013 5,169 1 View

DNA sequence data editing?

Do we need to edit (i.e. fill the gap, nucleotide edit) sequence data after alignment or not?Needed for further analysis (run with Arlequin, MEGA etc). If needed to edit after alignment (I have...

08 December 2013 7,885 22 View

PCR purification problem?

I am facing problem with PCR purification. I got good PCR band but after purification (by Qiagen purification kit) can't see good band in gel. Can anyone help? I want to sequence my sample.

11 November 2013 7,883 19 View