Can someone help with any tips on how to look for the gene islands, what software to use for alignments, and build the tree.
I have already constructed using only 1 primary gene in the island and compared it across different phylum. Now I would like to expand and look into all the genes present in the island or particular operon. Thank you
If you are using large number of samples, then you can align those genes using some multiple sequence alignment tool such as MUSCLE, and then construct the phylogeny using MEGA X software.
If you have only one sequence in question, you can perform NCBI BLAST search of the genes of interest. Then you can pick related sequences from there and perform phylogeny using MEGA X software.
You ask for distinct analyses. Let's split that into sections.
Multi-loci phylogeny. If your intention is to build a phylogeny of various genes, then you intend to build a multi-loci phylogeny. You should prior align each gene sequence separately then merge the alignments.
Ideally, I do this using a for loop with muscle moving from folder to folder. You can merge your alignments afterward using FASconCat (https://github.com/PatrickKueck/FASconCAT).
Then I suggest you test the best model for your phylogeny and build ML or Bayesian phylogeny. IQtree2 (https://github.com/iqtree/iqtree2) can do this in one step. Or use the classic combo Jmodeltest with RaxML.
Well, if you don't know your sequences first you gotta annotate them. You can search for island signatures using IslandViewer which integrates several other software (http://www.pathogenomics.sfu.ca/islandviewer/).
Most island predictions software rely on a finished genome, if that is not your case then you will have to manually look for IS sequences, tranposases, etc. Then you should aim for gff3 files as they are easier to parse.
Muhammad Shakeel Filipe Pereira Matteoli
thank you for the answers.
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