How to build a tree from SAM files?

Question

[Alina]

I mapped my reads to several references (reads of different species of viruses to different references), received SAM and BAM files.Is it possible to somehow construct a phylogenetic tree from them, i.e. first align all these reads from SAM files, and then get a tree based on this alignment? Or is it necessary first to assemble contigs from reads and only then proceed to alignment and tree?

Answer 1

[enyangqiao1]

It seems like you would like to do metagenomics analysis, maybe you can do novo assembly use these reads and then construct a phylogenetic tree from the assembled sequence.

[Alina]

You're right. This is a metagenomic study. But right now I'm focusing on just one family out of all the ones I've discovered. I thought it might be more efficient and reliable not to assemble, but to try with reads, because the assembled contigs turned out to be short, although the reads themselves cover a large reference gap.