Consensus phylogenetic tree?

More Ahasan Habib's questions See All

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 8,324 10 View

PCR amplification

Hi, Could you please clarify this query: if 426bp amplified for mtDNA D-loop (control region) and after editing/trimming primers finally get about 419 or 400bp. So is it correct if proceed final...

09 October 2014 7,964 4 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...

09 October 2014 4,815 3 View

How and in which stage during initial editing/trimming or after alignment do you trim the primers off from the sequence (full length)?

Hi, Would you please assist me, I need to double check. I use forward and reverse primers to get full length sequence. I amplified 426bp D-loop control region. But my full length sequence giving...

08 September 2014 2,470 10 View

Does anyone have experience with Sequence alignment?

Hi all, How to make sequence (DNA) in equal size after doing alignment in Clustal X? Sequence need to be equal size for Arlequin. thanks,

08 September 2014 5,581 13 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...

03 April 2014 5,859 6 View

How can you estimate the Nemf value and/or gene flow value (Nm)?

Is there any calculation to estimate the expected number of migrant females between/among populations per generations (Nemf), or can this be estimated by software? I can estimate pairwise Fst...

02 March 2014 762 9 View

Can anyone suggest how to prepare file for Arlequin for AMOVA?

I was trying to see the population structure of my study species. I collected samples from one study area (Sea) from one place. I did sampling from a total of 4 study areas (Seas) from each sea...

02 March 2014 4,410 7 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...

01 February 2014 8,260 20 View

Other than Arlequin, is there any software or online server recommended to do AMOVA analysis?

01 February 2014 7,306 6 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

Dana C Price

Depending on what you generated the trees with, SumTrees is a good tool for creating a consensus. It's written in python.

Ahasan Habib

thanks. i can see that, there is option in MEGA for it. but it is for individula tress (MP, NJ, ML). so how to comibe for these 3 methods for concensus!