Creating a multiple sequence alignment based on multiple genes.

Question

[matejasoretic]

I have run Panaroo on .gff files I obtained via Prokka from 160 genome assembly fasta files. Amongst the output I got from Panaroo were alignment files for each gene. I can use Clustal Omega or a similar MSA programme to obtain a MSA and phylogenetic tree from one of these files.

What would be the simplest way to obtain a MSA and phylogenetic tree based on several of these gene alignment files?

[Sasha]

To create a multiple sequence alignment (MSA) and phylogenetic tree based on several gene alignment files, you can follow these steps:

1. Concatenate the individual gene alignment files into a single file. You can use the cat command in the terminal for this purpose:

   cat gene_alignment_file1.fasta gene_alignment_file2.fasta ... > concatenated_genes.fasta
   

2. Perform multiple sequence alignment using Clustal Omega or another MSA tool. Here's an example using Clustal Omega:

   clustalo -i concatenated_genes.fasta -o aligned_concatenated_genes.fasta
   

3. Generate a phylogenetic tree using a tree-building tool, such as FastTree or RAxML. Here's an example using FastTree:

   fasttree -nt aligned_concatenated_genes.fasta > phylogenetic_tree.newick
   

   This will generate a phylogenetic tree in Newick format, which can be visualized using tree visualization tools like FigTree or iTOL. Please note that the code examples provided are placeholders and should be adapted to your specific file names and paths.

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