Computational Molecular Evolution turned out to be something different than I expected. I'll be finishing the last assignment tomorrow evening. It is a survey class. There was lots of hands on with several programs. Many techniques were discussed. I'll have an easier time getting up to speed the next time I encounter these things but I doubt I could use these programs by myself and get good results. The field is quite in flux. There are lots of good tools out there but they are changing all the time.
In the final assignment RevTrans 1.4 is mentioned to do DNA alignment. RevTrans 2.0 is in beta release now. It converts the DNA sequences into proteins, does the alignment on the proteins, then maps the DNA by codon to the aligned protein. The Center For Biological Sequence Analysis was upgrading their servers. Once I got the sequence I tried saving it to my (virtual) hard disk. The download process failed. I used copy and paste.
While I was told to save the file with the .fasta extension the file produced by RevTrans 1.4 was
the ClustalW multiple alignment format. EBI readseq was able to detect the real format just fine. The rule is let it autoselect. It was also able to write the PHYLIP4 format used by BioPerl.
I guess I am getting a feel for the range of tools available even if I don't know how to use them very well.
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