AOA sir. I am making phylogenetic tree of 168 proteins (40 for Arabidopsis, 41 for Rice and 87 for citrus) using this software. But, the software does not show all of the protein sequences and the alignment file also has some problem. Please suggest me any possible solution

@asifmolbio

3 ай бұрын

Its too many sequences probably beyond the capacity of a normal computer. Use less number of sequences or use a good computer

Sir I have performed phylogenetic analysis with various sequences in MEGA X but every time it shows invalid character found. Sir where is the problem what should i do to resolve this problem. I am waiting for your response

@asifmolbio

3 ай бұрын

send me files and error screenshort at asifalikalas@gmail.com

Assalam O Alaikum Sir! I am facing problem in visualising phylogenetic tree having 2908 sequences in it belonging to almost 140 plus plants using itol and related online software make the tree look so ugly because not even a single word is visible in it at default zoom level and zooming in will not capture the entire tree. Please suggest me anything useful in this regard. How can i visualise the entire tree at once without distorting the tree quality and information in it i.e. labels and their branching patterns.

@asifmolbio

4 ай бұрын

Wslam, i think your sequence number is too high. Why you took so many. You need to cut short your sequence first and why are you taking 140 + plants

@komalzia3576

4 ай бұрын

@@asifmolbio i am doing comparative gene family analysis in multiple plants and want to check the diversity in patterns of evolution in each plant.

@asifmolbio

4 ай бұрын

@@komalzia3576 it would not be possible for so many planet, you should only take model species for comparison

Very nice explanation 👌

@asifmolbio

3 ай бұрын

Glad you like it

What does the colour code of different amino acids represent after doing CLUSTALW?

@asifmolbio

3 ай бұрын

In Clustal W, the color codes of amino acids represent different properties or characteristics of the amino acids. For example: - Red: Small and hydrophobic amino acids - Blue: Acidic amino acids - Magenta: Basic amino acids - Green: Hydroxyl, sulfhydryl, amine, and basic side chains - Cyan: Aromatic amino acids - Yellow: Glycine - White: Any other amino acids These color codes help in visualizing and understanding the alignment of sequences in the Clustal W output.