MSA and Phylogeny after De-Novo-Assembly

Question

[j_susat]

Hey everybody,

I have a question regarding MSA and the construction of phylogenetic trees on the basis of contigs from a de-novo-assembly. So I have the contigs from my organism of interest and four reference sequences from NCBI which should be included in the phylogeny. But how to proceed from there?

I don't want to fill missing sequence parts in the contigs with parts from the references cause it could bias the resulting phylogeny. So is there any proper way to use the contigs as they are for an MSA?

Best and thanks in advance, Julian

Answer 1

[Rohit]

You could try to trim down the gaps in the sequences in the MSA - TrimAl can help.