PHYLIP Exercises

1. On watson.achs.virginia.edu, copy the files gstm.alib and gstm.nlib from /r0/seqlib/bioch508/phylip to a new directory.
   
2. Align the gstm.alib sequences using clustalw. Save the alignment in PHYLIP format (multiple alignment/output options) and be certain to save the sequences in "input order", not "alignment order" (multiple alignment/output options).
   
3. Use the readseq program to reformat the PHYLIP output as fasta output.
   
4. Use the mrtrans program to align the protein sequences in gstm.alib to the DNA sequences in gstm.nlib.
   mrtransl gstm.phy gstm.nlib > gstm_a.nlib
   (I will try to make an mrtrans WWW site to simplify this process.)
   
5. Use the readseq program to reformat gstm_a.nlib into PHYLIP format (gstm.nphy).
6. Use the protdist program to build a matrix of protein distances from gstm.aphy.
7. Use the dnadist program to build a matrix of DNA distances from gstm.nphy
8. Use the fitch and kitsch programs to build trees from the protein and DNA distances.
9. Use the protpars and dnapars programs to build trees from the protein and DNA alignment files.
10. Use the dnaml and dnamlk programs to build trees from the DNA alignment file.
11. Use the consense program to compare the trees.