I'm new to this so apologies if this question has been answered elsewhere:
I've recently sequenced 70 similar bacterial isolates using a MiSeq and assembled them using Spades. Each resulting fasta file has about 500 contigs.
My aim is to make each of these files into a single contig/scaffold, so that I can align with MUSCLE and then use FASTTREE to build the phylogeny.
Is there any way to do this?