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removing columns from phylip infiles

Jeremy Packer jclp100 at mole.bio.cam.ac.uk
Thu Nov 9 09:52:09 EST 1995


Hassan Badrane <hbadrane at pasteur.fr> wrote:
>ednah at mws4.biol.berkeley.edu (Huelsenbeck) wrote:
>>In article <47l8ns$441 at lyra.csx.cam.ac.uk>, Jeremy Packer
>><jclp100 at mole.bio.cam.ac.uk> wrote:
>>
>>> I often encounter the situation where I want to use only part of a 
>>> sequence alignment as a phylip infile. (for example to exclude all 
>>> postions where there is a gap in any of the sequences or where the 
>>> alignment appears uncertain). Until recently we had an editor which 
>>> could remove columns or blocks of columns from selected lines of the 
>>> alignment to generate the input file. Sadly it was very obsolete and the 
>>> only machine which could run it has died. Does anyone know of an editor 
>>> which can do this? We are mainly using Macs, but also have access to PCs 
>>> and UNIX( via telnet).
>>> 
>>> Many thanks
>>> 
>>> Jeremy
>>
>>You can use the program Word to delete columns.  For example, to delete
>>the third site pattern, you would (1) place the cursor between the A and C in 
>>species 1, (2) press Option and Shift at the same time (on a Mac), (3) while
>>pressing Option and Shift click the mouse after the G in species 3.  You will
>>have highlighted the third site pattern.  You can then hit delete to remove the
>>third site pattern.
>>
>>Species_1  AAC
>>Species_2  AAC
>>Species_3  AAG
>>
>>John Huelsenbeck
>>Department of Integrative Biology
>>University of California at Berkeley

Thanks indeed! I think this is the easiest of the suggestions, especially as we use Word 5.0 routinely!

Jeremy






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