Dear Researchers
While I am reconstructing the phylogenetic tree, I am getting an error message like this "Aligned sequences must be equal lengths (in line 3133). There was no error in the particular line. I have aligned the sequences from Clustal W and Muscle. I am using the Windows 10 operating system on my laptop. kindly give me an idea to resolve this issue.
By
Dr K. Sivasankaran
In Mega, this message usually means that one sequence is relatively short compared to other sequences or the phylogeny contains multiple short sequences that can not be aligned to each other as they are covering different regions (no common parts to align, at least compared to one sequence). This issue can be solved simply by deleting the sequence under inquiry.
Hope this will solve the problem
The error exist but you could not find it. The error maybe due to presence of "?" or "-", or somewhat which is not considered amino acid or nucleotide. I also got the same issue many time and error rate high and time taken then I used Geneious. The Geneious in restriction mode can also give a good error free alignment.
Regards
Abdullah
Dr K. Sivasankaran
I think you have to make all sequnces with the same length by adding (------) to the missing part of the sequence to be the same length when you compare two or more similar sequences of different length. After that you have to lock the sequences before saving them as fasta file that will be used in the Mega software.
Please feel free if you need more help
For a easy adding of (---) you can use Bioedit application and there, you save as .phy and just after, withaout close file, you save as .fas and that's it. Now you can open this .fas on Mega.
Dear Researchers
While I am reconstructing the phylogenetic tree, during the alignment step, I am getting an error message "Application error finalizing MUSCLE alignment: Unable to open file". How can I resolve this issue?
Thank you.
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