Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

Question

[Ayunndra931]

I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species), and they are using the contigs with the largest size. The contigs that they use contain markers such as matK, rbcL, and ITS. However my largest contigs doesn't have them. Is it possible for me to use the 2nd/3rd largest contigs that have those markers?

[dthorbur]

You need to provide more context. We don't know what kind of analyses you are doing, why you are limiting the analysis to just 1 contig, what assemblies you are using look like, etc...