Hi, can anyone recommend me some way of constructing a phylogenetic tree based on genome data assembled from isolates, my main question is can you compute the phylogeny based on the whole genome sequence or do you do it based on certain proteins? an which software can you recommend me for this?
I already searched for this and there are perhaps many ways to do it based on publications, but do someone does this in a specific way?
Constructing phylogenetic trees are topics that are addressed daily here, so it should not be hard to look for similar questions that other people have addressed. Just this week was a Help With Multiple Whole Genome Alignment. Aligning Over 400 Whole Genomes about using whole bacterial genome alignments as informative phylogenetic characters. It's not impossible to use whole bacterial genomes for phylogenetic data, but I think it's easier to select a handful of informative regions (coding or non-coding, such as ITS or IGS) and use those to infer a phylogeny.
This is a simplified version of what I do: (1) first choose your gene/proteins, (2) align them using a program and by eye, (3) make sure they are in a text format that phylogenetic programs can work with, (4) let the algorithms run on one or more (see here and here) phylogenetic programs, and (5) visualize your data.
I would recommend two books if you are new to phylogenetics: Tree Thinking, more on the theory side of things, and Phylogenetic Trees Made Easy, more on the practical data analysis side of things.
Just to add: for a standardized approach: Toward Automatic Reconstruction of a Highly Resolved Tree of Life -Ciccarelli et al Science 311 1283 PMID: 16513982. I haven't used but I heard a talk from NCBI that mentioned it.
Just to add: for a standardized approach: Toward Automatic Reconstruction of a Highly Resolved Tree of Life -Ciccarelli et al Science 311 1283 PMID: 16513982. I haven't used but I heard a talk from NCBI that mentioned it.