I would like to do genetic diversity analysis. Kindly suggest the name of important and free softwares for attractive NJ tree, dendrogram and PCA diagram?
- NJ tree is the tree building algorithm, it has nothing to do with how the final tree looks in appearance or attractiveness
- Dendrogram is the tree topology and it can be interchanged with any topology by the user, again nothing to do with attractiveness
>> But Figtree, dendrscope, iTOL, ETE3, Phylogeny.fr, PhyloT etc are the software/online tools
- PCA or similar plots can be made in R/RStudio and Python. Better to use R/RStudio, would be much easier.
As a supplement to the options given by Abhijeet Singh, you may consider using Molecular Evolution Genetics Analysis (MEGA; https://www.megasoftware.net/) for your NJ analyses, and Discriminant Analysis of Principal Components (DAPC) in CRAN R's adegenet package for your PCA analyses (https://adegenet.r-forge.r-project.org/files/tutorial-dapc.pdf), both which are available freely.
Hi Parmeshwar K. Sahu
For NJ tree and dendrogram analyses, MEGA can be used.
Regarding the PCA, you can try BioVinci (https://vinci.bioturing.com/user_guide). It is easy and simple to use it by dragging and dropping columns to their relevant positions. "The software allows scientists, without programming experiences, to quickly apply state-of-the-art machine learning techniques on their data and visualize the results to gain insights, otherwise, difficult to obtain."
You can see a PCA plot example here:
https://vinci.bioturing.com/panel/workset/build/principal-component-analysis
Good luck
Hi! Parmeshwar,
There are many softwares available to make phylogenetic trees.
May I know What do you mean by "attractive NJ tree"!!
It all depends on your data that you submit either sequences or Binary data (based on your gel images or character/properties)
If you use sequences - PHYLIP (PHYLogeny Inference Package), MEGA, Mesquite, ClustalX, TreeBASE, PAUP (Phylogenetic Analysis Using Parsimony)
If you use Binary data - PAUP, NTSYSpc, BNPP (Binary Near Perfect Phylogenetic tree reconstruction), Gusfield algorithm.
Good Luck!!
Dear Parmeshwar Sahu
I agree with suggestions given by Jetty Ramadevi. Moreover, you can also access Google; you may find what you desire!
Thank you!
Considering the complete answers from above, I may add SPLITSTREE (http://www.splitstree.org/) and GENODIVE (http://www.bentleydrummer.nl/software/software/GenoDive.html). They have some handy options for these analyses.
Good luck!
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