Hello biostars, I have a fungal genome assembly file, which has 987 sequence. I want to construct phylogenetic tree with related species.(10 numbers). Could anyone kindly recommend any suitable tools.
Your post is lacking details. You have 987 proteins, or 987 contigs? Protein or DNA tree? What does 10 numbers mean: 10 related species, or you want to do 10 trees? It is difficult for me to expend major effort, and I suspect for others as well, when you are willing to write only 2 sentences about your problem.
I would not normally do this using a pre-packaged pipeline as there are many things to be customized. However, since you seem to be new to this topic, here goes:
https://github.com/AstrobioMike/GToTree
It boils down to finding shared single-copy markers present in all species, aligning them individually, concatenating into a super-matrix, and building trees. A simpler but less accurate approach is to pick a couple of individual proteins (or rRNA) to build trees. I suggest you research this well before doing anything, as it is decidedly non-trivial.
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