How to construct colorful Phylogenetic tree using iTOL
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- Опубліковано 5 жов 2024
- #contruct #phylogenetic #researcharticle #iTOL #MEGA
In this video, I have explained how we can construct a phylogenetic tree using an online website. We can use this website for creating quality figures for journals. I have also explained how we can use mega software for creating newick file formats.
Previous videos Link:
How to download multiple sequences from NCBI- Lecture 1 Phylogenetic analysis
• How to download multip...
How to construct a phylogenetic tree and sequence alignment | MEGA X software -Lecture 2
• How to construct a phy...
In this video, we learned how to create file extensions for fasta format. Aligned the protein sequence using Clustal W alignment, and muscle alignment. Later on, we moved it for phylogenetic tree development.
Phylogenetic trees | Alignment | MEGA software
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How to make a phylogenetic tree in Mega software
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MEGA X: How to construct a phylogenetic tree
How to Make A Phylogenetic Tree From DNA Sequences | MEGA X Tutorial
MEGA | How to construct a Phylogenetic Tree? | Lecture 14 | Dr. Asif Mol Biology
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JSB #2 | Bioinformatics-2 | This is HOW to construct a Phylogenetic Tree in
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i TOL website
Thanks,
Finally, i have a good source of learning phylogenetics. 😊
Thanks
Very useful video Sir, I want to add some information like abundances of different groups in bar form with each label, splitting different labels in groups and denoted them with various colors, How to prepare dataset for that. plz make a video on that
Sure i will record soon
It is very useful. Thanks a lot from Vietnam!
Thanks, i am glad if you like it
Thank you very much for your video! it's very useful.
But, I have a question. How to make the taxon name have multiple styles? ex: scientific name of taxon in italic and accession number in bold?
Thank you!
can you mention the timeline (minute and seconds) in this video?
Many Mant Thanks for this video sir
Glad you like it
Super helpfull, thanks
Glad if it’s helping
I was looking similarly for this one.
Thanks a lot
Glad you like it
Very helpful - thank you!
Glad you like it
Nice video much helpful
Glad you like it
Great effort Dear Dr Asif can you make video on Multi locus sequence typing using 7 house keeping genes of bacterial species, using pubMLST and generating phylogenetic tree and its analysis. It will be appreciated work
Sure, please stay tuned
@@asifmolbio will be waiting appreciate your response
Well explained Sir ❤️
Glad you like it
please make a video on heatmap by using iTol
Ok i have noted down, please stay connected
@@asifmolbio sir i need it urgently
Thank you sir
Helpful video
Could you please tell me how to write clade in phylogenetic tress by drawing bracket
I couldn’t understand your question
Hlo Dr. Asif
May I ask why Bootstrap value are not shown when unploaded in iTOL , even though I saved the tree in Newick with bootstrap value?
Does iTOL have no options to visualize tree with bootstrap values ?
There is no bootstrap value option, but you can show branch length or distance in iTOL.
Alright 👍 🙏
The same problem I have, why no vlaue is showed? I didnt ubderstand your answer doctor@@asifmolbio
Aoa. sir can you make a video about EvolView for managing phylo trees
nice
Dr sab, AoA. hope you are fine. Do you have expertise in Structural Equation Modelling in Amos Software ?
Wslam, Naeem I don’t have
Sir, after saving the file in .png format when I open the image, the background appears black. i want to change it to white as seen in your case. Kindly help !!!
first paste in PPT (powerpoint) then export pdf and from pdf save figure at 300 dpi
ua-cam.com/video/ZnXuigqtMwg/v-deo.html
This video will be helpful
Sir i am unable to have the option to save the tree and when I try to process the construction of tree mega goes from windows instantly.
Quite confusing to me
How many sequence are you using for analysis? What i guess, Probably you choose 1000 bootstrap value, it need heavy processing and your computer doesn’t support heavy processing. Try to change the computer and try again
Sir, how to change only the species name in italic without changing all words including Genbank accession?
You need to do changes in original text file, which you used for newick format
@@asifmolbio thank you
Aoa Sir.
I have problem in uploading file because they show invalid branch lenghth and problem with Nod ID.
Sir to sort it out can you answer please
wslam, are you able to make a phylogenetic tree using MEGA ?
@@asifmolbio yes sir and i also change the mega tree into newick file.but when i uploading it to I-tol they showed error like this as i mentioned in last comment.
@@sajeelaakbar6553 when you made in MEGA does it show branch length?
@@asifmolbio G sir
thank you so much
Glad if it’s helping
Hi this is nice video. I am facing a problem in opening newick file. the error says Invalid branch length
J023019M18' I have 100 branches. could this be a problem with big number or something else? can you help? thank you
It may be due to method you choose for constructing tree and sequence of one entry in the file which you uploaded. Please check the sequence of J023019M18.
Choose 1000 bootstraps method to construct tree before saving newick file. If yoy still face problem send your text file (not newick) to me asifalikalas@foxmail.com
Hello Sir, When I upload the mega file for creating Nick, it starts running, but after some time, it disappears. I don't know what the problem is. Could you let me know if there is any sequence limit?....get me out of this problem so I can move to the next
Its due to computer memory crash, change computer or use less number of sequences and try if this problem occurs
Why is my tree in black background
it can be changed easily in the website
Hello Thank you so Muchh but I Have a Problem When i Save It In png Format the Background Turns Out Black How To save In Png format with White Background??
You can save pdf and then save it from pdf
@@asifmolbio Bootstrap Values Can't be Shown In iTOl Why?
Even software omega doesn’t show this information with in phylogeny tree. You just need to mention about boot straps value in material and method section (not in final figure)
@@asifmolbio Can't We Change Colors Of Labels In Mega 11 Itself??
@@heerabatool4240 not sure, but most probably We can
aoa. can you make a video on EvolView server please. thanku
Ok I noticed down your request, will upload soon stay tunned
thanku sir. i am thankful to you if a little soon. God bless you