This is such a basic question but I come from a non-bioinfo group so I keep getting different answers.
I was wondering if when making a phylogenetic tree whether you have to concatenate the chromosome and plasmids of the reference genome or if they're okay separate as a multi-fasta file?
Thank you
For this analysis I would doubt the direct use of the whole chromosome. As said in the previous answer about plasmid, the only this remaining is the genome. Use of the whole genome would increase the computation load and might cause discrepancy. Therefore how to genome is used is crucial point. If you are just pasting (concatenating) genome and plasmid sequences, his would most probably alter the correct phylogenetic inference.
In this case, a set of marker genes or COGs should be used. Further, the concatenation and partition analysis is to be followed for the phylogenetic reconstruction. The reason being different rate of evolution of different genes.
Phylogeny needs a broad knowledge base to be done properly. There are multiple theories and paths to follow depending on the main objective of your study. Usually orthologous genes are used to build phylogenetic trees. However, if you want a broader analysis there is a phylogenomics approach that can be used. As it has been well explained, including plasmids may affect your final tree so as not to reconstruct a true evolutionary history.
- Badges
- Science topic