How to perform Phylogenetic analysis using MEGA 11 software kzbin.info/www/bejne/jZecmZyAn92Bfpo

How to construct colorful Phylogenetic tree using iTOL kzbin.info/www/bejne/foXcY4FojKqJf7s

Watch these two videos you will understand completely

Like which other parameters

@@asifmolbio Thank you so much, I was able to do it

Sorry this is the only video on my channel, which is in Urdu. I will upload again with English language version

Hi, thanks for reaching out with a potential topic. I will surely record IA video on this and will upload soon

@@mamarlaeeqzia4667 may be it is reordered or rearranged

@@mamarlaeeqzia4667 check its position in all leaves

@@asifmolbio In your normal and circular tree, 2 domains are uncolored also. First one and 22. In my case, first one is uncolored, which is also first one in my Gene ID excel sheet.

Wslam you can apply for chinese government scholarship. if you want to know how to process your application you can search on youtube how to apply for chinese government scholarship 2025

Dear safwana, am sorry actually I never used the website you mentioned

Dont worry i am here to help. What is your field of interests

Glad if its helpful

It can simple help to show already made tool to make it color and even can show branching lengths and along with bootstrap values in the form of percentage.

If you are interested in more tools you can try For phylogenetic analysis using maximum likelihood (ML) with 1000 bootstrap replicates, several databases and tools offer more advanced settings compared to the MEGA software. Here are a few options: 1. **RAxML (Randomized Axelerated Maximum Likelihood)**: - RAxML is a popular tool for ML-based phylogenetic analysis. It allows you to set various parameters, including the number of bootstrap replicates. RAxML can handle large datasets efficiently and provides detailed control over the analysis. 2. **IQ-TREE**: - IQ-TREE is another powerful tool for phylogenetic analysis using ML. It supports a wide range of substitution models and allows users to specify the number of bootstrap replicates. It also offers a fast algorithm for bootstrap analysis. 3. **PhyML (Phylogenetic Maximum Likelihood)**: - PhyML is a straightforward tool for ML phylogenetic analysis. It provides options for different substitution models and the number of bootstrap replicates. PhyML is user-friendly and integrates well with other bioinformatics tools. 4. **PAUP* (Phylogenetic Analysis Using Parsimony)**: - PAUP* offers ML analysis and is highly customizable, allowing users to specify detailed parameters, including bootstrap replicates. It is a comprehensive tool but may have a steeper learning curve compared to other software. 5. **MrBayes**: - While primarily used for Bayesian inference, MrBayes also supports ML-based methods and bootstrap analysis. It is versatile and allows extensive parameter settings. These tools typically require command-line use, offering greater flexibility and control over your analyses. They are well-suited for advanced phylogenetic studies requiring detailed parameter customization.

How to calculate fold change FC, log2FC, Pvalue, Padj, Up and down regulated genes kzbin.info/www/bejne/fnmWfp-iabxojac

Here you go 👆

@@asifmolbiothis link is not helpful to me, I am working on network pharmacology problem, mostly my work is on gene ontology, KEGG analysis, gene expression not RNA seq

@@dr.manzoorahmad2682 two ways first you get your own transcriptomic data for second option i will share another link

How to analyze public RNA-seq datasets using iDEP tool kzbin.info/www/bejne/eHqYZ35pnL6XmtU

Glad if you like it

Yes no plagiarism

@@muhammadrizwansaleem590 thanks

Log fold change (log FC) is a measure used in various fields, particularly in genomics and transcriptomics, to represent the change in expression levels of genes between different conditions. It is calculated as the logarithm (typically base 2) of the fold change, which is the ratio of the expression level of a gene under one condition to its expression level under another condition. Mathematically, it is expressed as: \text{Log Fold Change (log FC)} = \log_2 \left(\frac{\text{Expression level in condition A}}{\text{Expression level in condition B}} ight) • A log FC of 1 indicates that the expression level of a gene has doubled. • A log FC of 0 indicates no change in expression. • A log FC of -1 indicates that the expression level has been halved. Using a logarithmic scale helps to manage wide ranges of fold changes and provides a more intuitive understanding of the relative changes in expression levels.

How to add logfc value if i have only one set of data

@@afreenkhan6008 if no control you cannot calculate fc hence cannot use this plot

@@asifmolbio can i get your email id I'll share uh my file please look once.

@@addisugetahun8418 whats error

How to avoid common errors/problems in SR plot data analysis tool? kzbin.info/www/bejne/inOWdGudZ7V5etE

Check this video if its helpful

Sorry it doesn’t

@@wizardlegend07 biorender

@@wizardlegend07 draw.io

@@wizardlegend07 but my best choice is powerpoint

How to make a graphical abstract using powerpoint | Complete workshop kzbin.info/www/bejne/pJvVY6yBp9CWhaM

Yes ideally 200-250 bp but upto 400-500 is also okay

What about 135pb or 150pb

@@loverofimrankhan945 still okay

Now i am doing functional analysis of these genes, Transformation etc..

GWAS or characterization? Looks great can go for publication

@@asifmolbio Genome-wide identification, Now doing function analysis, over-expression vector

@@asifmolbio genes belong to light receptor gene family, so will check the expression under different light conditions.

Sounds good

Thanks for suggestion, i am planning

Most welcome!

So nice of you

Thanks for the visit

To check the Animal Cytology Database for a detailed protocol like the Lysosome Tracker experiment in macrophage cells, follow these steps: ### 1. **Access the Database:** - Go to the Animal Cytology Database website or portal where it is hosted. - Log in if credentials are required. ### 2. **Search for Protocols:** - Use the search bar and type keywords such as "Lysosome Tracker," "macrophage cells," or "lysosomal staining protocol." - You can also navigate through the sections dedicated to specific cell types or experimental methods. ### 3. **Filtering and Refining Search:** - Filter your results by cell type (e.g., macrophages), assay type (e.g., fluorescence microscopy), or specific dyes like Lysosome Tracker. - Refine the search by publication date or relevance if the database allows for advanced search options. ### 4. **Accessing the Protocol:** - Once you find the relevant protocol, click on it to access the full details. - Download or save the protocol as needed. ### 5. **Using External Resources:** - If the protocol is not available in the database, consider checking other scientific protocol repositories like **Bio-protocol**, **Addgene**, or **JOVE**. - You can also search published articles on platforms like **PubMed** or **Google Scholar** for the specific experimental method. ### 6. **Contacting Database Support:** - If you are unable to locate the protocol, reach out to the database's support team or consult with colleagues who might have access to this protocol. ### General Outline for Lysosome Tracker Experiment in Macrophages: If you do not have direct access to the database and need a general overview of the experiment, here’s a simplified protocol: 1. **Cell Preparation:** - Culture macrophage cells in appropriate medium until they reach the desired confluence. 2. **Lysosome Staining:** - Incubate cells with Lysosome Tracker dye at a concentration recommended by the manufacturer (e.g., 50 nM to 1 µM). - Incubate for 30 minutes at 37°C. 3. **Washing:** - Wash cells gently with warm PBS to remove excess dye. 4. **Fixation (Optional):** - Fix cells with 4% paraformaldehyde for 10 minutes if live-cell imaging is not required. 5. **Imaging:** - Observe the stained cells using a fluorescence microscope with the appropriate filter set for Lysosome Tracker (typically green or red fluorescence). 6. **Analysis:** - Capture images and quantify lysosomal distribution or fluorescence intensity using image analysis software. If you need the exact protocol, it’s best to refer to the Animal Cytology Database or other specialized resources.

Yes it does

A bioinformatics guide to Metabolomic Data analysis interpretation kzbin.info/www/bejne/gWPUiqiCaNFjeZY

here is a video of metabolome

if still videos are not helpful, one to one live session can be booked at forms.gle/aEVUtAzrbSHxeN659

hamry hi samples ka data hota hai yeh

How to draw a principal component analysis (PCA) plot easily? kzbin.info/www/bejne/g4rMdWN4n96hicU

Dear MD Manat, Here is video for PCA analysis

For docking i will upload soon

Thank you sir. Hopefully you will make the video soon. Eagerly waiting for this.

Dear Subeka Dass, i have started a project to explore about cancer. Many more detailed videos will be posted. Thanks for suggesting this topic

Yes really interesting

@@monishamitra151 yes its free

Thanks Zohaib, stay in touch

@@HarshNegi-f6p Glad if its helpful

Thanks Zohaib, May Allah bless you too

Glad if it is helpful

Thanks and glad if its helpful

Sure, thanks for suggesting this topic

I will record

Sure, thanks for suggesting a potential topic.

You’re welcome

:p

Thanks

Thanks

Standard deviation of gene of interest Standard deviation of endogenous (house keeping) gene Delta critical threshold

Glad if its helpful

Welcome

I have also responded to you via email. Please share the code you tried and let me know if you are using Windows?

Thanks Aaiman