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tutorials:eccb_t2_badasp [2012/09/08 15:26]
romainstuder
tutorials:eccb_t2_badasp [2012/09/08 16:15] (current)
romainstuder
Line 26: Line 26:
 We want to identify the residues making differences between the **isoforms 1** and **isoforms 4** of the V-type proton ATPase 116 kDa subunit a. We want to identify the residues making differences between the **isoforms 1** and **isoforms 4** of the V-type proton ATPase 116 kDa subunit a.
  
 +First, visualise briefly the multiple alignment in Jalview. (File "badasp_eg.fas" in the badasp folder.
  
-<code> 
-cd ./badasp  # Folder of installation 
-</code> 
  
 Execute **badasp** by importing the multiple alignment in FASTA format ("badasp_eg.fas") and activating the interactive mode (i=1): Execute **badasp** by importing the multiple alignment in FASTA format ("badasp_eg.fas") and activating the interactive mode (i=1):
-<code>python badasp.py seqin=badasp_eg.fas i=1</code>+ 
 +<code> 
 +cd ./badasp  # Folder of installation 
 +python badasp.py seqin=badasp_eg.fas i=1</code>
  
 Badasp will ask for the associated tree, in newick format ("badasp_eg.nsf"): Badasp will ask for the associated tree, in newick format ("badasp_eg.nsf"):
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 => Press enter => Press enter
  
-# We need to split the tree on the node 21, so we need to define two groups from the children nodes 20 (= VPP1 subfamily) and 19 (= VPP4 subfamily) .+# We need to split the tree on the node 21, 
 +so we need to define two groups from the children nodes 20 (= VPP1 subfamily) and 19 (= VPP4 subfamily) .
 => Press M, then enter.  # Manual grouping => Press M, then enter.  # Manual grouping
 (Tree displayed) (Tree displayed)
-Choice? [default=Q]:  c  # We collapse node+Choice? [default=Q]:  c  # We collapse nodes
 Node [default=0]: 20 Node [default=0]: 20
 => Type VPP1, then Press enter => Type VPP1, then Press enter
  
-Choice? [default=Q]:  c  # We collapse node+Choice? [default=Q]:  c  # We collapse nodes
 Node [default=0]:  19 Node [default=0]:  19
 => Type VPP4, then Press enter => Type VPP4, then Press enter
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