ClustalW | Phylogenetic Tree | Lecture 3, Part 3 by Dr. Muhammad Naveed

How to make Phylogenetic Tree using ClustalW, Branch length, Bootstrap value, Branch Leaf.Phylogenetics is the study of evolutionary relatedness amongst organisms. The
genetic relationships between species can be represented using phylogenetic trees.
Advances in genomics have enriched the range of computational methods available
for assisting experts in building these trees. Among other methods, these trees can
be built by comparing genetic sequences of various species. The current
implementations of multiple sequence alignment have limitations that prevent them
from constructing accurate phylogenetic trees when sequences with low similarity
are contained in the dataset. The purpose of this project is to modify the ClustalW
sequence alignment algorithm so that it can be used to construct a more accurate
tree when highly divergent sequences are present. The modifications to the
existing algorithm consist of two parts. First, the highly divergent sequences are
identified within the dataset by analyzing the pairwise alignment scores. Next the
guide tree, which is used to determine the order that the sequences are aligned in, is
modified so that the highly divergent sequences are aligned last. Mitochondrial
genome sequences of species with known phylogenetic trees are used as a dataset
for testing. ClustalW and PHYLIP provide a variety of methods for constructing
trees using the multiple sequence alignment as input. These trees are compared to
the known tree to determine which version of the algorithm provides a more
accurate tree. The results of this study show that the modified version of ClustalW
produces a more accurate evolutionary tree in the majority of all the tests. In
addition, the modified algorithm is more capable of correctly placing the highly
divergent sequences in the phylogenetic tree.
#Phylogenetics_Tree #ClustalW #MSA

[@sabgaminggamer2256]

thanks sir.. for uploading this.

[@tahiraaslam4365]

Excellent way👍👍👍👍keep it up ❣️

[@khannajeeb1218]

Thanks sir I get many information from your knowledge but sir your spiking is very fast
But sir I think full to you

[@Prof.Dr.MuhammadNaveed]

will slow down

[@abdurrasheed2143]

Sir app ny mujhy Sara bioinformatics samjha deya .thank u very very much.

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@amjadyousaf6006]

Thank you so so much sir for this channel

[@ayeshamalik4679]

Is there any statistical method to compare the results of MEGA7 tajimas test substituon pattern estimations and pairwise distance please expalin this?

[@LaibaSajjad-dz2oo]

Thori speed slow rakh laty to ho jata sir!😢

[@myrasheed-]

phlygram ko article , thesis mai use krny pr cite kesy karen gy isy??

[@shanzaybabar7293]

best way to teach sir g..... it all reminds me of my bioinformatics classes by you. still remember each n every lecture... (y) u keep rocking we r supporting :)

[@Prof.Dr.MuhammadNaveed]

Pleasures

[@rudrashettiashwinkum]

Pls give the lecturer on Metagenomic DNA analysis using MG-RAST tool.

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@syedbukhari1124]

Bioinformatics at its best (y) keep rocking sir

[@Prof.Dr.MuhammadNaveed]

stay blessed

[@khannajeeb1218]

Nice sir

[@Maryam-nn6ex]

Sir please prepare on cytoscape also

[@ayeshanoor9045]

Thank you sir .excellent way of teaching.sir plz upload MEGA lectures.

[@Prof.Dr.MuhammadNaveed]

Next Friday

[@nimramushtaq3803]

Excellent work.
Sir please also guide the phylogenetic tree on megaX

[@Prof.Dr.MuhammadNaveed]

Yes already in list and you may find here coming weeks as Lecture 14

[@ideasthoughts8303]

great. keep it up naveed bhai.

[@Prof.Dr.MuhammadNaveed]

I will try my best

[@NOMIZYGOUS]

Good job, Kindly make a lecture about MEGA tool and Ensembl Genome Browser too

[@Prof.Dr.MuhammadNaveed]

Noted dear will share soon

[@akan1033]

could you guys please help me how to do multiple sequence alignment using HomoloGene?
i m new in bioinformatics and stuck in homoloGene page after selecting four sequences of my gene of interest from NCBI homepage and dont know what to do after it..
will be very thankful!

[@Prof.Dr.MuhammadNaveed]

Watch my lecture 1, 2 and 3 all about this

[@ZainMughalVlogs]

Sir maza aa gya

[@Prof.Dr.MuhammadNaveed]

pleasures and good luck

[@hilalahmad9016]

How to submit sequences at NCBI, PLZ make video about this

[@Prof.Dr.MuhammadNaveed]

sure dear noted

[@3223243651212]

THNKS SIR

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@farihajavaid4653]

I have a question sir....can we construct phylogenetic tree by using protein sequence? Which one is more authentic by using DNA sequence or protein?

[@Prof.Dr.MuhammadNaveed]

can do but DNA sequence algorithm are more reliable

[@dr.adnanrasheed9122]

Sir, I have different genes group in Table. How I can make phylogenetic tree by using genes name?

[@Prof.Dr.MuhammadNaveed]

do individually

[@IkanPediaMalang]

Sir i would very happy if you give lecture in english.. thank yu..

[@Prof.Dr.MuhammadNaveed]

sure dear our next series is in English

[@ashfaqmohmand9165]

Your way of teaching is best..
But try to slow your speaking speeking

[@Prof.Dr.MuhammadNaveed]

sure dear

[@saqibaagha7665]

Please also tell us about drawing map of genome of genome .

[@Prof.Dr.MuhammadNaveed]

noted

[@saqibaagha7665]

@@Prof.Dr.MuhammadNaveed please tell us how to use OGDRAW for drawing of circular map of genome .

[@DrZahidMumtaz]

You will also like this tutorial. ua-cam.com/video/yhjVtkU8rFU/v-deo.html

[@ussefrassln8253]

good job but can u speak slowly