remove.dists

The remove.dists command removes distances from a phylip or column file related to groups or sequences listed in an accnos file.

accnos

The accnos file contains a list of the groups or sequences you would like distances removed for. For example:

final.test.accnos contains:

F003D000   
F003D002
F003D004       
F003D142   
F003D144 

phylip

The phylip option is used to specify the name of the phylip formatted distance file you would like to remove distances from.

The final.tre1.weighted.ave.dist file contains:

11
F003D000   
F003D002   0.219014    
F003D004   0.405823    0.285439    
F003D006   0.311126    0.227599    0.197012    
F003D008   0.246074    0.221351    0.341801    0.220774    
F003D142   0.381307    0.350587    0.175825    0.199702    0.331989    
F003D144   0.380843    0.3943  0.350766    0.278915    0.37678 0.239005    
F003D146   0.277258    0.300362    0.331904    0.242542    0.239576    0.246918    0.160718    
F003D148   0.308621    0.299937    0.303805    0.254025    0.27361 0.246377    0.15778 0.120112    
F003D150   0.315133    0.307792    0.206429    0.209389    0.27078 0.179998    0.260263    0.217917    0.195339    
MOCK.GQY1XT001 0.64778 0.69245 0.769817    0.703035    0.61892 0.715547    0.662322    0.613735    0.648762    0.716918    

mothur > remove.dists(phylip=final.tre1.weighted.ave.dist, accnos=final.test.accnos)

creates a final.tre1.weighted.ave.pick.dist file:

5
F003D006   
F003D008   0.220774    
F003D146   0.242542    0.239576    
F003D148   0.254025    0.27361 0.120112    
F003D150   0.209389    0.27078 0.217917    0.195339    
MOCK.GQY1XT001 0.703035    0.61892 0.613735    0.648762    0.716918    
       

column

The column option is used to specify the name of the column formatted distance file you would like to remove distances from.

U68590 U68589 0.67
U68591 U68589 0.7559
U68591 U68590 0.8011
U68592 U68589 0.6585
U68592 U68590 0.6528
U68592 U68591 0.7849
U68593 U68589 0.6953
U68593 U68590 0.6383
U68593 U68591 0.7741
U68593 U68592 0.6041
U68594 U68589 0.7109
U68594 U68590 0.7233
...

If you want to remove sequences U68589, U68590 and U68592.

mothur > remove.dists(column=amazon.dist, accnos=amazon.test.accnos)

amazon.pick.dist contains:

U68593 U68591  0.7741
U68594 U68591  0.7554
U68594 U68593  0.5503
U68595 U68591  0.7067
U68595 U68593  0.7143
U68595 U68594  0.7086
U68596 U68591  0.7491
U68596 U68593  0.4869
U68596 U68594  0.3689
U68596 U68595  0.7266
U68597 U68591  0.7627
U68597 U68593  0.4155
U68597 U68594  0.5047
...

Revisions

  • 1.30.0 - First Introduced