Entering edit mode
2.7 years ago
triplee0305
▴
10
Hi all,
I tried to use MEGAX to build a phylogeny tree for 60 species with 5 genes (but not every species has all 5 gene sequences being available).
After reading some suggestions online, I first aligned each gene and then concatenated the resulted sequence alignment (missing gene are represented as '?') for each species. All these steps were performed in MEGAX. With the resulted sequences, I tried to align it again before constructing the final phylogeny tree. However, MEGAX prompted up error when aligning the concatenated sequences. The error message said "Application error finalising MUSCLE alignment: Unable to open file".
Please anyone knows how to solve this error? Or I misunderstood something?
Thank you!
Without even knowing why MEGA X error happened, I don't see what good will come out of realigning concatenated sequences that were already aligned. And I can see lots of potential for bad things happening.
So I can directly construct the final phylogenetic tree based on the concatenated sequences? And would you mind sharing your insight on the bad things that would happen? Thank you!
There are no alignments after concatenation, only before. Assuming you have done the previous steps correctly, I suggest you go ahead with the concatenated alignment without any modification.
The concatenated alignment is almost guaranteed to change if you realign it, and it is not supposed to. So that's bad for sure. It is meant to be a set of individual local alignments that are concatenated together into one big global alignment.
What exactly were you hoping to achieve by realigning?
I actually don't know what to expect from realigning the concatenated sequences. It is my first time to build a phylogenetic tree. After reading several (confusing) suggestions online, I feel like to first align each gene and then concatenate them, then align again and finally build the tree. Thank you for clarifying the steps!!
May it help others facing the same question. I first aligned each gene following the this protocol and then concatenated the alignments as this tutorial suggested.