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removing columns from phylip infiles

Hassan Badrane hbadrane at pasteur.fr
Thu Nov 9 05:25:31 EST 1995


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
>
>* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *                      
>                       John & Edna Huelsenbeck
>johnh at mws4.biol.berkeley.edu             ednah at mws4.biol.berkeley.edu
>             http://mw511.biol.berkeley.edu/john/edna.html
>* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *


very interesting thanks

Hassan




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