I want to do project on phylogenetics on hiv subtype-1. but how I start the project on this, what tools are apply on this?
I want to do project on phylogenetics on hiv subtype-1. but how I start the project on this, what tools are apply on this?
Phylogenetics is a complex field that requires a lot of background knowledge. You do not provide any information about your dataset so I cannot help, but I'll give you a super quick overview of how I would produce a publication-quality phylogenetic tree using likelihood-based approaches. I would recommend reading up on the literature.
Errors or improper/inappropriate settings at any of these steps will produce an unreliable tree. Push-button pipelines often produce suboptimal results.
I am happy to provide more detail if you (or others) need it.
Your answer is very well worded and give a round explanation of phylgenetics. I want to take a chance and ask about some tips. If I have a good quality alignment and want to estimate which sequences is more ancestral to the other one, which algorithm is more appropriate to answering that question ? A neighbor joining one or one that is based on UPGMA. I haven't really found satisfying answers in the literature. All I found was an explanation of the different tree building methods and nothing on the merits of choosing between methods to answer specific evolutionary questions.
Thanks again
Both NJ and UPGMA use distances to construct a tree. NJ trees are not necessarily rooted, whereas UPGMA (as it's a clustering approach) are. The biggest difference is that UPGMA assumes a constant rate of evolution across the lineages i.e., a molecular clock; because this is often violated in empirical datasets, this approach is usually considered sub-optimal.
Since the NJ tree will be unrooted, sequences/taxa will be polarized based on how you perform the rooting. The placement of the root is one of the most difficult parts of estimating a tree. Depending on your question, an unrooted NJ tree may be appropriate for what you need. Alternatively, I'd recommend estimating a high-quality tree using a Bayesian approach such as BEAST which places a prior on the age of the root.
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Hi mahi, your post is very poorly written and researched, such posts are often closed quickly. Please rework your post and read some introductory materials on phylogenetics first.
I would start by reading like 10 review articles on HIV and then follow from there to research papers, which are more close to your desired topic.
What is actually diffrence between NJ tree and UPGMA tree.
Secondly, I want to construct NJ tree from genetic distance values. Please suggest me some online softwares, with their input data format, because I am facing many problems in data entry.