I aligned a sequence using MEGA X (GUI, mac) and I want to turn it into a phylogenic tree.
I exported the alignment to .meg file but when I "open a file" and choose "analyze" it will only give out the first sequence. I tried a .mas file and the same issue. I tried deleting the first sequence and that ended up with only the second sequence as an output. I wondered if my MEGA was glitching so I tried a previous alignment and there was no issue. I opened the faulty file and the working one in https://hexed.it/ to see if there was some end code that I was missing. It's possible that the hex D8 is causing my issue, but I don't know what to do with that info. I tried exporting to .fas and .nexus and when analyzing them they both came up with error: Invalid amino found, expected an amino but found '. Issue is when I search for ' I can't find it. The weirdest thing is that it doesn't seem like the files are messed up because when I click align there is no issue, just the analyze. I tried on another computer and got the same issue.
I am very frustrated and I have no idea how to fix this. The alignment took 8 hours so I really hope the issue isn't that I need to do the alignment again.
Thank you all!
