Practice of Phylogenetic program

DNA or peptide Sequence of Beta-lactamase of pBR322

國家衛生研究院GCG巨分子序列分析服務:
 SeqWeb program (http://gcg.nhri.org.tw:8003/gcg-bin/seqweb.cgi)
Similarity searching Blast search  and blast aligments

Reference searching String search database1 and  String search database 2

Sequence manager: input seqnence

GrowTree: Related sequence

If more unrelated sequence using Phylip program

1. Comparison:  Pileup(txt) pileup(gif) and save as Pileup.html or Pileup.txt

2. GeneDoc for data reformat:

• New file; Import; Input from "clipboard" copy from Pileup.html & paste into  clipboard[choose GCG(MSF)]; save as Pileup.msf; export; choose "select all" and "philip format type" to produce Pileup.phy
• New file; open file  Pileup.txt save as Pileup.msf; export; choose "select all" and "philip format type" to Pileup.phy

3. Phylip:

• Rename Pileup.phy as "infile" and run protdist.exe (for peptide) and dnadist(for DNA) to produce" outfile "
• Move out "infile" and rename the "outfile" to " infile"
• Run "infile" using Neighbor.exe to produce " outfile" and " treefile"

4. Run textedit.exe or word.exe: replace ":-" of treefile  by ":" (no negative value"-")

5. Run Treeview (C:\program file\Rod page\treeview\treeview.exe), open treefile to see Tree Unrooted Tree, Slanted Cladogram Tree, Rectangular Cladogram Tree, and Phylogram Tree

6. Revised Tree in powerpoint.exe or other graphic program