@@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.
The problem is solved. The first one remain uncolored, because the gene name was the first one in the excel sheet. It considered the first name as the title name. When we give the title name in the excel sheet like Gene and Gene ID. And the upload the excel file then it colors all the genes
in circular tree ... u have added excel sheet in layer section... what type of data excel sheet contain? what we have to add because my color section is not coming
Respected sir kya ap cnsknowall pe b bana dyngy? Wo b aisa he hy per us main account nah ban pa raha.us main account banana seka dain.hopfully ap reply dyngy
Could you please teach it from the beginning? what is the format of the file and what data needs to be uploaded while drawing a phylogenetic tree. Thanks.
Suggest me some database through which by using maximum likelihood with 1000 bootstrap parameters applicable instead of mega database. As in the above explained database not even showing any type of parameter settings.
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.
Aoa sir ap kaisay hain please suggest any scholarship only research related. In Business administration or finance or accounting for PhD. I have completed course work here in Pakistan please
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
thank you so much for these videos. its really helpful
Glad if its helpful
bro how to make the metadata file. can you give the link of video in which you made that file?
if you can watch the video, i have already demonstrated this all in video.
I constructed the tree but it didn't include the first gene when color the leaves and branches
@@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.
The problem is solved. The first one remain uncolored, because the gene name was the first one in the excel sheet. It considered the first name as the title name. When we give the title name in the excel sheet like Gene and Gene ID. And the upload the excel file then it colors all the genes
in circular tree ... u have added excel sheet in layer section... what type of data excel sheet contain? what we have to add because my color section is not coming
kindly help me?
Its just metadata like groups of species for example from rice can be A and from arabidopsis can be B
Respected sir kya ap cnsknowall pe b bana dyngy? Wo b aisa he hy per us main account nah ban pa raha.us main account banana seka dain.hopfully ap reply dyngy
Dear safwana, am sorry actually I never used the website you mentioned
Could you please teach it from the beginning? what is the format of the file and what data needs to be uploaded while drawing a phylogenetic tree.
Thanks.
How to perform Phylogenetic analysis using MEGA 11 software
th-cam.com/video/Wf9hiJjxNH8/w-d-xo.html
How to construct colorful Phylogenetic tree using iTOL
th-cam.com/video/HTy2N2WEVIY/w-d-xo.html
Watch these two videos you will understand completely
Suggest me some database through which by using maximum likelihood with 1000 bootstrap parameters applicable instead of mega database.
As in the above explained database not even showing any type of parameter settings.
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.
Aoa sir ap kaisay hain please suggest any scholarship only research related. In Business administration or finance or accounting for PhD. I have completed course work here in Pakistan please
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