How To Analyze Phylogenetic Trees | Interpret Bootstrap Values and Sequence Divergence 👨🏻‍💻🧬

Simple Guide on How to Build and Interpret Phylogenetic Trees
#Cladogram
#Bootstrap_Values
#Sequence_Divergence
#molecularbiology
#bioinformatics
#biotechnology

[@yokaisamaful]

Straight to the point and well presented. Thank you for your video.

[@MadisonMunarPhD]

thanks😊

[@yokaisamaful]

@@MadisonMunarPhD Most welcome

[@chiomastellaanyairo1825]

After struggling for 36hrs, I finally got a breakthrough!! Thank you so much, Sir.

[@MadisonMunarPhD]

You're welcome! 😊

[@LA-cm9uo]

Thanks sir! You have earned yourself a subscriber.

[@MadisonMunarPhD]

Awesome, you're welcome and thank you! 😊

[@fishfish20]

I love the presentation.

[@MadisonMunarPhD]

Thank you😊

[@anisad9702]

Thank you😊 very helpful

[@MadisonMunarPhD]

You're welcome 😊

[@wanderingfish]

Very informative po since I am interested to work on fish phylogeny.

[@MadisonMunarPhD]

thanks😊

[@bakashabajacob3130]

Thank you👏👏🤝🤝

[@MadisonMunarPhD]

You're welcome 😊

[@yokaisamaful]

I'm new to phylogenetic analysis and i wanted to ask you about how to choose the sequences from NCBI, i have the 16s rRNA sequence of my sample and i want to perform a phylogenetic analysis to identify it. Do i blast my sample sequence and save the accession number of the 10 strains with the highest similarity % to export later or how do i go about it?

[@MadisonMunarPhD]

Hello Yokai, yes that's right, you can have a BLAST analysis of your 16S rRNA sequences and you may opt to include 10 organisms in your phylogenetic analysis. I have also a video on how to do proofreading and quality trimming of raw DNA sequences 👉kzbin.info/www/bejne/nWqYZZudjsp_h68, and DNA sequence assembly 👉kzbin.info/www/bejne/e5rbiWZmr999eac, all the best😊

[@yokaisamaful]

@@MadisonMunarPhD Thank you for your answer, if you do not mind, i have another question regarding Bootstrap values. what does it mean when a branch does not have a bootstrap value?

[@user-nq9pt2ko2c]

This is very informative and organized. I would humbly request your slides, sir. Thank you

[@MadisonMunarPhD]

send me an email, [e-mail]

[@jonengobeh3588]

Thanks u❤

[@MadisonMunarPhD]

You're welcome 😊

[@SufyanKhan-qv4js]

Hello, sir very informative video. Sir, can you tell me that how can we copy the MSA result from MEGA X to MS Word for publication?

[@MadisonMunarPhD]

Hello Sufyan, thanks😊 👉download SnapGene Software (www.snapgene.com/) to be able to view the saved MSA and save into PDF file. Save your MSA in FASTA format in your desktop and then open using the SnapGene Software, open print preview and save in PDF format😊

[@ashwiniashwini7494]

sir can you please help me to interpret phylogenetic tree of terpene synthase which i constructed using MEGA11?

[@MadisonMunarPhD]

Hi Ashwini, sure just send me your cladogram maybe through my messenger. Provide a simple objective so I may know what to look at the tree.

[@sunflowers5990]

Sir, i want to ask. If the branch isnt supported with high boostrap value such as 1% or 2%, can we say the relationship remain unknown?

[@MadisonMunarPhD]

Hi @sunflower5990, if the bootstrap value is below 50% the grouping is not well supported, you may check your alignment if there are gaps and unaligned sequences, all the best!😊

[@emitezuka5514]

Can I ask you something sir? Why I get slightly different tree everytime I change the sequence (same species with different accession number) ? It seems like we can manipulate the phylogenetic tree

[@MadisonMunarPhD]

Hi Emi, I hope I can take a look at your cladogram for me to evaluate it, however, based on your question, it seems you are using different accession numbers for the same species which leads to a slightly different tree everytime, I would suggest that you check the information about the sequence by clicking on the Accession Number, make sure that the reported sequences are the same, for instance if the two species with different Accession Numbers were both 16S rDNA sequence, if the DNA sequence reported were different most probably it will not be aligned thus will be interpreted as a different species. So make sure you are using the same DNA sequence or gene in your phylogenetic analysis.

[@emitezuka5514]

@@MadisonMunarPhD thank you very much for your reply and explanation sir. Yes, they both are the same tufA sequence, and its make me confused. Do you know any journal or book that I can read for understanding this topic sir? thank you

[@MadisonMunarPhD]

Hello again Emi, if it's the same gene I also wonder why it makes a different tree, you may also check the direction of the sequences, you can simply observe the alignment and if the two similar DNA sequence were not exactly aligned most probably their direction is different, you can change the direction of the sequence by clicking "DATA" then "REVERSE", this will change the direction of the sequence.

[@emitezuka5514]

@@MadisonMunarPhD thank you very much sir, I've got a lot of information from you.

[@MadisonMunarPhD]

welcome, good to hear from you Emi😊

[@sumnilmarwa4519]

What can be the reason for low bootstrap values?? How to avoid it

[@MadisonMunarPhD]

Hi @sumnilmarwa4519 , make sure your aligned sequences have the same lengths and direction

[@nurtenyilmaz430]

good day sir, Thank you for your video, 'm new to phylogenetic analysis and i wanted to help mi for analyze my PhD thesis DATA. I have 128 lactic acid bacteria strains isolate from raw and ferment products. all of isolates are Lactobacilluscaea; lactococcus enterococcus lactococcus leuconostoc. I have a BLAST analysis of my 16S rRNA sequences and 128 isolate, but ı don't know in phylogenetic analysis. I wonder if there is a friend I can cooperate with who can do this analysis for me.

[@MadisonMunarPhD]

Hi @nurtenyilmaz430, for phylogenetics analysis using the MEGA software you can watch this video 👉 kzbin.info/www/bejne/govZin-PrZdsipI, if you have questions, please feel free to comment, all the best! 😊

[@unknownbeliever4660]

how can i learn more to learn about interpreting phylogenetic trees?

[@MadisonMunarPhD]

hi, do you have specific concerns regarding the phylogenetics analysis? please let me know☺️

[@kashishkamra4667]

How inversion, look like in alignment file ?

[@MadisonMunarPhD]

Hello Kashish, you may observe sequence inversions by visually checking your alignment, I usually include duplicates of the same sequence for control.

[@kashishkamra4667]

@@MadisonMunarPhD actually m confused in identifying in the alignment . Btw thanks 😊

[@azi5443]

good day sir! thank you po for this informative video. medyo naguguluhan po ako sa tree na nagawa ko, can you help me po to interpret the phylogenetic tree of neuroglobin sequences that I constructed using MEGA X? thankyou very much sir!

[@MadisonMunarPhD]

Hi Azi, you're welcome, please send me message through my messenger

[@nurshahiraruslan9644]

Thank you sir ( ╹▽╹ )

[@MadisonMunarPhD]

thanks😊

[@kinkpelionel3287]

Hello, sir very informative video. Thank you so much . sir can you please help me to interpret phylogenetic tree of lactoferrin gene which I constructed using MEGA11. If yes, May I have your messenger count ? Thank you in Advance.

[@MadisonMunarPhD]

Hello Kinkpe Lionel, sure please send me a message through my messenger (Madison Munar)

[@ojeniyifiyinfoluwa8251]

Hello sir. I want to humbly request for your slides on phylogenetics analysis

[@MadisonMunarPhD]

Hello, please send me a message through my messenger- Madison Munar

[@MadisonMunarPhD]

Hello, please send me a message through my messenger- Madison Munar