removing columns from phylip infiles

Huelsenbeck ednah at mws4.biol.berkeley.edu
Wed Nov 8 20:36:42 EST 1995


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

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