Hi @Asha1,
I just would like to point out that it is very difficult to generate a reliable global sequence alignment across all fungi using fungal ITS (I assume you are referring to fungi). Thus, ITS data are often not appropriate to generate global phylogenies. However, if you are only analyzing closely related taxa, e.g. within genera, you are likely okay. I’ve listed a few good references below. I am sure others will have additional insight too.
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If you’d like perform phylogeny-based analyses on your ITS data, then I’d highly recommend using Ghost-Tree. More details can be found here.
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As an aside, you may also want to consider ITSxpress, to pre-process your data.
I would also highly recommend this article:
- Nguyen et al. 2015: Parsing ecological signal from noise in next generation amplicon sequencing.
-Best wishes
-Mike