I am trying to build phylogenetic trees using Mega-X from the seq codes provided by the Lab in ab1 format. However, there is some problem or maybe (???) I am doing something wrong in MegaX. I am quite sure that I am following the protocol properly, however.
When aligning the seq code (fasta format) with similar species and even type material of the presumed identified species from BlastX, I can't get anything aligned properly. When I got results from Blast, I selected top 5 accessions, and some type material, added my sequences into a single fasta file, loaded it into MegaX to align, tried various combinations of ClustalW and Muscle, by my sequences are very different from the supposedly closely related accession. What is wrong !
To make things worse, I have uploaded these sequences into GenBank today so hope they are not bad sequences that are badly converted from Abi to fasta).
Hope u have time to check
Regards
Stephen
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