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Remove.dists

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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