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cd /home/bsm4/rstuder/Dropbox/ECCB2012/Tutorial/badasp # Folder of installation

# Run badasp

python badasp.py seqin=badasp_eg.fas i=1

# Ask for a tree
Looking for treefile badasp_eg.nsf.
Tree: ['seqin=badasp_eg.fas', 'i=1', 'nsfin=badasp_eg.nsf']  <ENTER> to continue

=> nsfin=badasp_eg.nsf

=> Press enter

Display Tree, with two groups of sequences:
V-type proton ATPase 116 kDa subunit a
- VPP1 = VPP Isoform 1 (8 genes)
- NVL = VPP Isoform 4 (3 genes)

Rooted Tree (1000 bootstraps). Branch Lengths given. 21 nodes.  <ENTER> to continue.
=> Press enter


Tree is rooted at node 21 => perfect
=> Press 0, then enter.

 *** Tree Menu *** 

Sequence Data are already imported => we quit the menu.

Choice [default=Q]:  q 
Quit Tree Menu? (y/n) [default=Y]:  y

#*# Grouping Summary #*#

Currently 0 groups. (11 Orphans)
=> Press enter

We need to split the tree on the node 21, so we need to define two groups from the children nodes 20 and 19.
=> Press M, then enter.  # Manual grouping
(Tree displayed)
Choice? [default=Q]:  c  # We collapse node
Node [default=0]: 20
=> Type VPP1, then Press enter

Choice? [default=Q]:  c  # We collapse node
Node [default=0]:  19
=> Type VPP4, then Press enter

Choice? [default=Q]:  Q, then enter  # We collapse node
Quit Tree Edit? (y/n) [default=Y]:  y

#*# Grouping Summary #*#
ENTER> to continue.
Choice for Grouping? [default=K]: K, then enter
Keep Groups? (y/n) [default=Y]:  Y, then enter
Save groups? (y/n) [default=Y]:  y
Name of Groupfile? [default=badasp_eg.grp]:  enter
Write Group Names? (y/n) [default=N]:  N
Use badasp_eg for output filenames? (y/n) [default=Y]:  enter
Use these parameters? (y/n) [default=Y]:  enter


Making Ancestral Sequences - Variable PAM Weighting
Reading PAM1 matrix from jones.pam

# #Start computing
Saving Ancestral Sequences in badasp_eg.anc.fas...  <ENTER> to continue.
Method BADX needs query but none given. Drop BADX from specificity methods? (y/n) [default=Y]:  n
Method BADX needs query but none given. Use sequence 1 (vpp1_HUMAN/Q8N5G7)? (y/n) [default=N]: y 

Calculating ['BAD', 'BADN', 'BADX', 'SSC', 'PDAD', 'ETA', 'ETAQ'] scores... (849 residues) ...win(0)  <ENTER> to continue.
...Done!  <ENTER> to continue.
...win(0)  <ENTER> to continue. # (many times !)
Output additional, filtered results? (y/n) [default=N]:  y
Name for partial results file? [default=badasp_eg.partial.badasp]: enter 

Output subfam 1 (VPP4) details (pos,aa & win)? (y/n) [default=Y]:  y
Output subfam 2 (VPP1) details (pos,aa & win)? (y/n) [default=Y]:  y
Output BAD results? (y/n) [default=Y]:  
Output BADN results? (y/n) [default=Y]:  y
Output BADX results? (y/n) [default=Y]:  y
Output SSC results? (y/n) [default=Y]:  y
Output PDAD results? (y/n) [default=Y]:  y
Output ETA results? (y/n) [default=Y]:  y
Output ETAQ results? (y/n) [default=Y]:  y
Output Info results? (y/n) [default=Y]:  y
Output PCon_Abs results? (y/n) [default=Y]:  y
Output PCon_Mean results? (y/n) [default=Y]:  y
Output QPCon_Mean results? (y/n) [default=Y]:  y
Output QPCon_Abs results? (y/n) [default=Y]:  y
Filter Rows by Results VALUES? (y/n) [default=Y]:  y
Min. value for BAD? [default=-6.708333]:  
=> New value = "-6.708333"? (y/n) [default=Y]:  
Min. value for BADN? [default=-6.708333]:  
=> New value = "-6.708333"? (y/n) [default=Y]:  
Min. value for BADX? [default=-3.500000]:  
=> New value = "-3.500000"? (y/n) [default=Y]:  
Min. value for SSC? [default=0.000000]:  
=> New value = "0.000000"? (y/n) [default=Y]:  
Min. value for PDAD? [default=-0.297619]:  
=> New value = "-0.297619"? (y/n) [default=Y]: 
 Min. value for ETA? [default=0.000000]:  
=> New value = "0.000000"? (y/n) [default=Y]: 
 Min. value for ETAQ? [default=0.000000]:  
=> New value = "0.000000"? (y/n) [default=Y]:  
Min. value for Info? [default=0.424111]:  
=> New value = "0.424111"? (y/n) [default=Y]:  
Min. value for PCon_Abs? [default=1.000000]:  
=> New value = "1.000000"? (y/n) [default=Y]:  
Min. value for PCon_Mean? [default=5.000000]:  
=> New value = "5.000000"? (y/n) [default=Y]:  
Min. value for QPCon_Mean? [default=9.375000]:  
=> New value = "9.375000"? (y/n) [default=Y]:  
Min. value for QPCon_Abs? [default=0.000000]:  
=> New value = "0.000000"? (y/n) [default=Y]:  

BADASP Partial Results Output (badasp_eg.partial.badasp) ... Done!

#LOG    00:23:06        BADASP V:1.3 End: Thu Sep  6 13:59:24 2012

### Analysis

Open the file in your spreadsheet (or cut&space).

The columns are separated by a tab.

Color the "BAD", "BADN" and "BAD" columns with a conditional formating, with value > 3.

In Jalview: