I need to construct a robust phylogeny based on the core genome of the strains. I have around 61 genomes of the strains. I want to know which bioinformatics tool is needed ?
Follow these steps:
1. Genome Assembly: Start by assembling the genomes of your 61 samples from the raw sequencing data. This can be done using genome assembly tools such as SPAdes, Velvet, or IDBA-UD.
2. Core Genome Alignment: Once you have assembled the genomes, you need to identify the core genes shared among all samples. Tools like Roary or PanX can help you identify the core genes by comparing the annotated gene sets across genomes. These tools generate a core gene alignment, which represents the conserved regions across all samples.
3. Multiple Sequence Alignment: Next, perform a multiple sequence alignment of the core gene sequences obtained in the previous step. Tools like MAFFT, MUSCLE, or ClustalW can be used for this purpose.
4. Phylogenetic Tree Construction: Once you have the multiple sequence alignment, you can construct a phylogenetic tree based on the aligned core gene sequences. There are several software packages available for this task, including RAxML, IQ-TREE, and FastTree. These tools use algorithms such as maximum likelihood or Bayesian inference to estimate the evolutionary relationships and construct the tree.
5. Tree Visualization: Finally, you can visualize and annotate the constructed phylogenetic tree using tree visualization tools such as FigTree, iTOL, or Dendroscope. These tools allow you to explore and customize the tree display, add metadata, and highlight specific branches or clusters of interest.
Hope it helps
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