MEGA | How to construct Phylogenetic Tree? | Lecture 14 | Dr. Muhammad Naveed
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- Опубліковано 16 лип 2020
- Phylogeny refers to the evolutionary history of species. Phylogenetics is the study of phylogenies-that is, the study of the evolutionary relationships of species. Phylogenetic analysis is the means of estimating the evolutionary relationships. In molecular phylogenetic analysis, the sequence of a common gene or protein can be used to assess the evolutionary relationship of species. The evolutionary relationship obtained from phylogenetic analysis is usually depicted as branching, treelike diagram-the phylogenetic tree. Historically, the use of phylogenetic trees was restricted more or less to the study of evolutionary biology, and to disciplines like systematics and taxonomy. However, with the advent of sequencing and the widespread use of cladistics, the use of phylogenetic trees has pervaded many branches of biology and beyond. Construction of phylogenetic/evolutionary trees is now widespread in many areas of study where evolutionary divergence can be studied and demonstrated; be it pathogens, biological macromolecules, or languages.
#MEGA #Bootstrap #PhylogeneticTree - Наука та технологія
The best and the perfect lecture by you, Sir. I just followed the guidelines or steps with you and constructed a phylogenetic tree without any hurdle. Thank You so much sir for such kind and guidance. God bless you more and more.
Great job!
You always prepare precise and perfect tutorials. God bless you Sir.
MashaAllah. Very informative. Thanks alot. A jaisy legends k hoty hue hm apny research work ko behter bana sakty hai
Thank you so much sir very informative lecture
Thank you very much for this video, it's help me lots ☺️
Thank you sir for this informative lecture. Sir please make another video on phylogenetic tree best designs, as well as interpretation of the phylogenetic tree.Thank you so much Sir!
Well done, Keep it up Doctor sahab...
In sha Allah
This is worth appreciable👍... thankyou
welcome
Very informative and basic video ..
Best and perfect lecture sir, I must say. Thank you
welcome dear
@@Prof.Dr.MuhammadNaveed Aoa sir I have trouble in one thing
I am uploading my sequence in mega 11 and it kept saying " invalid character found" please help me out I have my defense next week
Perfect explanation.. good learning
Glad you liked it
very well explained ...you save my time ...thank you so much sr
Pleasures and welcome dear
simply described, well done
Many thanks!
Hello sir i have one query i want to know which software i can use to open mega files. I am not able to open the file after export in mega please guide me. Thank you
when you'll export the file select ''All files'' whether, in any format, your file will open. nd Mega software itself is used to open mega files.
Great work sir 😊😊you expalined very nicely
welcome and pleasures
Sir, thanks for the wonderful tutorial.
You are most welcome
Insert sequence from fil k option k bad world ki file upload ni ho ri.. box open ho ra unknown data file format
Good job sir ALLAH apko kamyabi de ❤️❤️
Ameen and stay blessed
Thank you so much, sir!! Badi mushkil se nikala aap ne
Very informative. thank you sir...
Most welcome
Very Helpful. Thank You Sir
You are most welcome
Thankyou sir it is an informative lecture keep it up 👍✨
pleasures and good luck
Good evening Sir... I like all your videos..they are very informative....
pleasures
Thanks, sir u help me a lot with regard to this software.
Glad to hear that
A job well done, Sir.
We're still waiting for our English version.
sure dear just need finish this series in native language
Sir how can we labelled sections and clade in Mega
Great video 💯. Thanks a lot !
glads it helps you
Thank you so much sir❤️❤️
Hi
Sir hope you will be fine. can you please tell how to calculate interspecific and intraspecific distances for a large data set?
Thank you sir.. n plz upload more detailed basics of phylogenetic tree analysis
what kind of detail dear
Sir if no matches are found after blast then what to do
How to select outgoup specie for phylogenetic tree
Very informative sir thank you so much
Glad to hear that
Is it necessary to take the same length sequences for different species while constructing a phylogenetic tree
not necessary
Thanks alot sir...!!
Sir when I do blast of my sequence...I get the different sequences with homology...But to construct a phylogenetic tree I also have to include my own gene sequence how can I do that sir
yes you have to add yours sequences
Hello sir
Greetings..
I have gone through ur most videos,very informative.
Sir i used mega6 for phylogenetic tree construction, in the end i found a tree was constructed but a value is coming 0.05, where this value is strick out (kati hui h), i tried many times, different ways. So it seems the tree made wasnot correct. I didn't know where i may be wrong.
Plz help me to find out
its ok but try to use megax where no such issues
informative and helpful video. . . but I want to know how we can change the style of our tree?
Sir, I am aligning sequencing in MEGA format, but after opening the same file, I am getting message "Align Sequences must be of equal length". How to fix this problem?
remove sequence tag with zero or have no sequence
Sir, incase protein sequences, then can I use Maximum likelihood method rather than neighbor joining method for phylogenetic tree construction?
yes can use this as well
@@Prof.Dr.MuhammadNaveed which one is better for protein for tree construction?
what should be considered while choosing the maximum likelihood or neighbor joining tree method
your data or design of tree
Thanks a lot sir, all your vedios are helpful for students like us. Sir I was using mega 7 for phylogentic construction but the file for alignment is not getting imported what may the problem sir?
look formatting of sequence file
Very informative video sir
welcome dear
Aoa, i have performed Mega X to form phylogenetic tree. i also have design pairwise genetic distance, but please give a lecture to read table formed by using mega X.
sure and noted
I have learned lot from ur lectures. Love from Srinagar, Kashmir
welcome dear stay blessed
I guess it's kind of off topic but does anyone know a good website to stream newly released movies online ?
@Fox Vincenzo lately I have been using flixzone. Just search on google for it :)
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@Maximo Quinn Thanks, signed up and it seems like a nice service :D Appreciate it !
Can I use SSR data in mega software for phylogenetic tree?
yes
Thank you so much for your guidance as I'm going to interpret my research results. These lectures help me a lot. You got another subscriber. Keep doing the good work. May Allah SWT bless you with best reward as you're teaching students like us free of cost.
pleasures to hear and stay blessed
You will also like this tutorial. ua-cam.com/video/yhjVtkU8rFU/v-deo.html
Sir how can i construct a phylogenetic tree from phytochemicals or pubchem id by using mega?
here need sequences that might be from plants where got phytochemicals
Sir!! Amino acid sequence mai jab tree banana ho to uska bhi ClusterW alignment karengay k nahe..
yes can do
Great sir
welcome dear
Sir Can we construct phylogeny of randomly selected 10 plants rbcL sequences with each other ?? Is it scientifically correct??
yes you can
thank you sir
Glad it helps you
Sir when I did the blast of my 16 s rna sequence it's showing 99% similarlity with all the the complete genome sequences . Is it correct? I mean is it possible for a partial sequence to show similarity with all the complete genomes when we blast. If yes can we do the phylogenetic tree analysis of that.
Thankyou sir 🙏🏼
yes possible
Sir i have one question plz tel me wgat the benefit of phylogenetic tree ruther then history
biologically more authentic
If we do blast of specific seq...we have multiple hits...how we know which hit is the best one..
the best query coverage and identity score
Jazakallah
sir suppose company send to us sequence of one protein related to different species, so we blast one by one of each species for example we have Danio rerio species we find the similarity and select more than two similarity than next we have salmo salar by blast we select more than two similarity and so on we have 20 species sequences from the company if we blast all one by one than we will get many similarity and make the phylogenetci tree that tree will be very large...so in this
case what we should do ?
Oho! Mam you here...
He is best one to deliver the lecture related to bioinformatics
No problem you get 5 homologous from blast of each sequence then in total now you have 100 and MEGA will give you results and other way go with half of species or go with 3 homolog
Thanku so much sir for this informative video 🙏 sir if possible I request u to make a video on UPGMA and maximum likelihood method and other methods nd it's significance where we can use these methods.... I saw a lot of videos but ur way of teaching is excellent totally grab the whole content in simple words thanks alot sir 🙏😊
note and sure will do
You will also like this tutorial. ua-cam.com/video/yhjVtkU8rFU/v-deo.html
good explanation
Thanks and welcome
Commendable sir!
Please start series on NGS
sure
Thankyou
You’re welcome 😊
@Dr Naveed Muhammad Dr Sab how to interpret the tree please explain this in new video what we concluded from tree
AMAZING JOB SIR
welcome
very informative video
gald to hear that its helps you
Nice presentation sir
Thanks and welcome
what is difference between clustaW anlignemnt and muscle alignment ?
Not a big difference just have minor difference at algorithms but both are very well cited and recognized
sir you selected 1000 bootstrap value but after the Phlyogenetic tree is formed so at roots 100 bootstrap value is mentioned..why?
1000 is at algorithm but in results it always about 100 or less like 50 because it based on 100 time matching rule
This 100 bootstrap value is the % bootstrap replicates where you see in the node. It means, that node where you can see 100 or where branches emerge is very very good and statistically well support. Because it reveals in all the all the replicates. This para is not simple; let me explain this in a very simple way, You are orchard to select citrus fruit, you are just getting data of 100, then farmers stop you, you have now 100 samples from the orchard , you are using the test statistic on these 100 by repeating the test again and again, repeating mean, sampling by replacement, and now the question is how many times out of 100, you are observing the same sample(in your case the same branch) during the repeation of the test. Suppose if you get 100 out of 100 of a branch, it means these sequences in the braches are supporting each other and fit very well. But if your square is less than 70 or 50 out of 100 then I would say your branch is not well fit and the identification seem to be statistically not supported.
Very informative sir.... Can u do a tutorial on multigene phylogeny?
sir i faced a problem. while doing multiple alignment of sequences it takes upto 6 hours but still no results appears plz guide me.
then means your sequences size is too large or try to perform on anyother PC
You are a wonderful teacher
Pleasures
@@Prof.Dr.MuhammadNaveed dear sir, if you don’t mind and have some spare time can you please explain how can one clean raw sequence data in bioedit. In your Video of bioedit you didn’t tell how to delete start or end of sequence or deal with the noises inside the sequence.
@@Humeera1 it is very simple just pick wrong base from chromatogram then select delete option to delete it
@@Prof.Dr.MuhammadNaveed sir I tried to highlight the start and end of sequence and pressed the delete on my keyboard but it didn’t. May be I m not doing it on the right way or missing some step or having a bug in my software. Don’t know
Thanks for the teaching in the most easyway possible
@@Prof.Dr.MuhammadNaveed sir one thing more I wanted to tell. Urdu lectures are great and easy to understand as there are bundles of English videos. Please do continue in Urdu. We will be obliged. Stay blessed
plz make a video how we can use sequence data send by company many students confused how to use file send by company...otherwise data we get from database we can easily get everything and managed how to use data which is downloaded from database
Agreed and sure will make a lecture on. Our Bioedit lecture have some kind of information about this lec 13
Aoa sir! Hope you are fine. Thanks alot for this video. Could you please guide me that if we blast our query sequence and we didn’t get any matchable sequence in the blast neighter spp level nor genus or ecen family level in case of plants. Then what should we do to do a phylogenetic analysis to construct a tree?
If there is no match, then why you want to make a phylogenetic tree. Although, most probably issue is with your sequnce
Thank you sir. In order to fulfill the research work objectives have to find the phylogenetic relationship? Then could it be possible to get the phylogenetic relationship? Is there any other way?
@@bushraabbasi7690 no best way is by MEGA or clustalW
@@bushraabbasi7690 Extract DNA from three repeats. Do PCR separately, run the gell, check the band's size, any two bands on the gell or dimers or any low quality, If all is well, then send these three samples to the company for sequencing along with primers, get the sequences, remove primers mismatches and manually check all these three sequences, any SNP or any mismatch replace with the correct one, if you, remove these and see other two sequences if there are gctgc then replace, then go for BLAST, but do blast with type species, if you can get any species than it is fine, otherwise just blasting one sequence and getting none, I assume that you did error during sending samples to company or you have send the wrong sequences or some other PCR or contamination issues or sequencing runs failures,
Amazingggg
Glad it helped
Sir after all process OK ka option nii aaata.
then problem in your input sequences
Respected Sir, how can we modified the phylogenetic tree which we have constructed in MEGA-X. For example how to color the tree, how to use sequence of taxa as an out group for tree and using different sections of species. Please it is my humble request to make video about this.
at last step of mega when built tree then all these option available to trim your tree
thankyou so much sir everything is explained in a very nice way. kindly guide me what will be the scenario if aligned sequence is taken from clustle omega. is there any change or the steps will remain same. kindly guide me.
do same
Thank you so much sir
Maximum likelihood method vs upgma difference kia h please explain.
difference in their scoring and matrix
Great job sir, just go for whole genomics sequence data analysis of any bacteriL DNA..
You are doing whole genomic sequences from various pathogens isolated from infected human blood, and you are getting a lot of information, Look, But this information just indicate the source from where they have come from. But what about traceback of the certain sequence[From where? How it is here? Which strain?, how to link that sequence with the disease. The source is human blood samples but it should not lead us to the presumption that the human blood caused diseases. Whole genomic sequence data analysis, database is still incomplete may be a new crona type bacteria is there, can this whole genome isolate that, each technology has its own limitation, morphology first, then whole genome sequences, then verification via qpcr or other methods, then we sure then yes this strain is responsible for this
@@AqleemAbbas We can use only one software means like...
Galaxy
usegalaxy.org
If sir teach students about assembly type tips of the microbial DNA seq..it will be a great contribution
@@probioticgenomics1014 You should have a heavy computer having Linux, then I can tell and explain advanced molecular tools, But for now, this may be useful for your data. huttenhower.sph.harvard.edu/galaxy/
@@AqleemAbbas Yes, we have workstation and Linux too...thanks for link..
Assalam o alaikum sir
Phylogenetic analysis krte waqt issue aa raha ha ap Mje bta dain k aisa q ho raha ha analysis krte waqt jb mega file upload krte hain to all sequence select hoty hain including name name ko remove kro to aik seq ko unselect krna parta ha q k AGR sb seq ko select kren to name b automatically select ho jata ha
just unselect name sequence as in video
You will also like this tutorial. ua-cam.com/video/yhjVtkU8rFU/v-deo.html
Sir what's the difference between clustal W and muscle allignment.
Both are same but differ only in the algorithm
The main difference is the algorithm. Moreover, ClustalW does the global alignment(whole sequence) whereas MUSCLE does a combination of both global and local(part of the sequence).
i need your lectures about bioinformatics for BS/Msc students. Thanks
sure dear and just write an email on dr.naveed@ucp.edu.pk for this regard
Aoa sir plz if u know about response surface methodology plz make a video on it..it is related to stats ...if u can guide me from where i can get detail video about it...i have to use it in my thesis...by the way very informative lectures
sure will make on it
Sir, please make video regarding how to make colourful phylogenetic tree using MEGA - X software. It will be your most kindness
Ok I will try
Awesome
welcome
how to download Mega X software?
from google
How to construct the tree by using different bacterial sequence
mega and change algorithm accordingly
How can we make polygenetic tree for multipul genes. Like OCTs transporters.
you can do it in various ways. You can use APEX
@@Prof.Dr.MuhammadNaveed is it necessary to have branch length scale 0.1? I am getting 2.1 is it ok??
You said, mutliple genes and genes are different, so blast them separtly, and get the more similar sequences from NCBI and make a phylogenetic tree,
@@cndoo Convert this into percent, there is an option in the software, this is the bootstrap value, you can click the option it will convert into percent, percent shows bootstrap actually these are statisicall repeats, how percent your sequence is similar to others, if less than 70% your branch and that clade is statisically not valid
@@AqleemAbbas sorry i forgot mention. Same gene of different species ( human and rodents). And i tried by amino acid sequence.
Nice one sir g I have a problem faced in mega, when i construct a tree than some clades have low value what's the problem.
Its mean variation in sequences so you can edit to remove those dissimilar sequences by BioEdit
@@Prof.Dr.MuhammadNaveed how sir.. have you upload a video about editing a sequence in bioedit...
@@qamarzaman2669 ua-cam.com/video/h6Ox9WOTBJ4/v-deo.html
You swift from NJ to parsimoney or vice verce. And when you are going for tree, you need to check the models, for example, go to analyis preferences, select models for example in my case jukes canter model work but in your case it should be different, Other suggestion your consensus sequence remove mismatches or snps or any other error, correct it then blast to get the most similar sequence, in blast always view the distance tree which will tell you or give you an idea, where your query sequence match, and then run mega and do the same as I suggested above
@@Prof.Dr.MuhammadNaveed Dr. I have also suggestions for you. Kindly use 16 S sequences forward and reverse, make a consensus sequence and then paste, this consensus sequence to BLAST, and then to MEGA, in this way the tutorial will be unique and will reach to every student. The way you are doing is not new, it is common, as thousand of tutorials are in the youtube. What I mean, you teach from scratch will be appreciated.v
Sir can u please tell us how to build a tree using outgroup???
everything same just add a different specie sequence in your sequence list then rest same this will come as outgroup
@@Prof.Dr.MuhammadNaveed thanks for ur reply sir..... sir,,, I'm building tree of tamarix species using maturase K as barcode,and took polygonaceae as outgroup, the problem is that bootstrap values in tree is 2,5,4 etc.... eventhough I took 1000 bootsrap in parameters
Sir pairwise alignment is complete but multiple alignment take lot of time, why is this so?
because its have more sequences
@@Prof.Dr.MuhammadNaveed ok thank you sir,I will try it again if that is the issue.
Role of phylogenetic in biotechnology iski mujhy pdf chahiye
sir you have taken only one sequence what if i took so many then how many sequence we choose form blast data like you select 6
yes you may take 10, 15 up to 100 sequences
@@Prof.Dr.MuhammadNaveed sir i have put 10 sequence from different species of same gene and then i did protien blast then i have choose 100 sequence from blast which is the result of blast then i have upload that file into megax but there so much divergence in my sequence wont able to make phylogenetic tree
@@Prof.Dr.MuhammadNaveed I just want to ask you how I do make phylogenetic tree from diffrent species for same gene.
@@labeenausmani9696 same case was with me, so if you have many sequences do blastp one by one and than choose two or three higher identity similer sequence from each species and than you can construct phylogenetic tree,suppose u have species salmo salar and do blastpchoose three similer sequences and than you have homo sapiens sequence do blastpand choose three similer sequences, than make a phylogenetic tree than you will see uwill not have more divergence species in your tree , dont choose more than five from each species. hope u get ur answer
@@shahnazsalamat1271 thank you so much i will try then i will let you know.
Actually Sir I have no idea would you come Hazara university at 4th international conference on 15 September 2022 so this way I was missed this conference I want to meet you, anyway Inshallah I well meet you very soon.
How to italic the species name in mega
just click on specie in try to become editable
Thank you sir for your response..
But when choose italic font, all the numbers and species name converted in italic. I want only species name in italic and accesion number in normal format.
U r super sir
Alhamdolillah
sir agar cladogram banana ho tu kaise banaen ge
plz make a video within 2 to 4 days because main ne poora youtube chan mara hai par mujhe kahin cladogram nai mila
noted but its take time
Aoa sir secondry phylogenetic origin ka kya matlab ha?
could you elaborate your query
@@Prof.Dr.MuhammadNaveed Sir larvae of echinoderm is bilateral and adult radial which shows their secondary phylogenetic origin.I want to know what did they mean by secondry phylogenetic origin
Make a vidoe on RNA sequencing
noted
Plz tell Me what should I do
??
How I add outgroup sequence in phylogenetic tree please respond
good
Welcome