Suppose we are performing a phylogenetic analysis among different fungal species and we wanted to see how closely our species of interest is related with the other species across different families belonging to the same Order. After performing the multiple sequence alignment, can we extract the aligned regions (which are common across all the species) and use only that much length of nucleotides for constructing the phylogeny (and remove the unaligned regions)?
For e.g. if the length of our sequence of interest is 700bp and only 200-300bp is aligning with the other retrieved sequences, then can we extract 200bp aligned region and use only this much portion for constructing the phylogeny? Or the sequence of the entire length is required for phylogenetic analysis?
Unaligned regions should not be used to infer phylogenies. So, yes, you can extract only the aligned regions.
Yes you can, but do not remove gaps that are generated after alignment within the aligned sequences.
You can remove a taxon which is not aligning (usually this doesn't happens unless your sequences in reversed) with other sequences, and you can also trim either ends of the aligned sequences.
if you have more queries i would recommend you to go check out my youtube channel "Tepin's Lab" i made some videos related to these stuffs which can give you better understanding.
Of course you can, but i recommend that you submit the entire sequence (700bp) to genbank
You can trim sequence from both the ends and can take aligned part but should not remove nucleotides from the middle. For example your sequence of interest is aligning with subject sequence from 1-60 bp then not aligning for 50 bp and again aligning from 110-150 bp. In this case you can take either from 1-60 or 110-150. You should never remove those middle 50 bp just for getting for aligned portion.
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