Dear almighty all, Recently, I want to make a phylogenetic tree for few species, but phylogenetic tree making tool I know are aviliable for genes only. Thus, I wounder if you can tell me any software or tool, or method that can couduct this analysis.
Thank you very very much!!!
The differentiation between a species tree and a gene tree isn't a hard and fast cutoff. Some people do a single-gene tree, declare it is reflective of the species tree, and call it a day (this is a bad idea). Today, because of widespread availability of whole genome sequences of many organisms, most people do what is called phylogenomics. There are a number of different ways of doing this, but probably the most straightforward is to concatenate the sequences of multiple genes/proteins together (after doing multiple sequence alignment individually) and putting that as your input to a phylogenetics estimation program (like RaxML, FAstTree, etc) just as you would any other alignment.
However, this gets complicated. There are lots of things to consider such as rate of evolution in the different genes, gene selection (paralog, detection, etc). Put simply, there are about a million ways to go wrong, and there isn't necessarily a standard well defined pipeline for analysis like we have in say, human genome analysis. My recommendation is to go to the literature first and read the papers of people doing similar things to what you want to do to get a feel of the programs they used and some of the parameter choices they made. If possible do some testing to replicate their work if the underlying data is publicly available. Then work on your own data. If you happen to have some molecular evolutionary biologists or phylogeneticists at your institution take one out for coffee to chat about your project or maybe start up a collaboration to learn from them. Its like any other skill, it is really a good idea to get some hands on experience with some expert guidance.
For building any tree from sequences first you need to align those sequences. and use that alignment to build tree. As you want to build the tree bases on core sequences, first you need to find core sequences.
It is hard to manually find all those proteins common to all species of interest. For that you need to go for any Pan-Genome analysis pipelines.
You need to concatenate all the core genes of a species to one large sequence and then go for alignment using ClustalW (slow) or MUSCLE (fast). and build tree using same alignment by respective tool.
If you have GenBank or annotated fasta files BPGA can build a Neighbor joining tree or UPGMA tree based on that.
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so, on what basis do you want to build a tree?
I heard one method called concatenated phylogenetic analysis of protein sequences, of which my undestanding is to do MSA for all protein sequences of homologous genes, and then combine and analyze the results of MSA to generate the phylogenetic tree. But I do not know how to do it or whether it works.
If I am not wrong taxonomic analysis is perrformed based on DNA or protein sequences. Which material you want to use to make the tree?
Protein sequences of course. I believe this will be more accurate.
You can practically use any type of DNA sequences to build phylogenetics. Let me know if this is what you are asking for.
Actually I want to use their protein sequences, I think this will provide more accurate result.
any particular protein you know or set of proteins or all conserved core proteins?
All conserved proteins. I'm afraid others may not work for the species I want to study.
Try using the protein sequences of housekeeping genes, such as DNA/RNA polymerase genes. Those genes are usually conserved and are able to distinguish the ancestral relationship for the species you study. Unless, you are looking particularly a gene that you are interested. I have heard that MrBayes uses Bayesian Inference for phylogeny and is able to produce accurate results but I myself still use conventional methods like ML and MP and have not tried it out yet.