removing columns from phylip infiles

Brian Foley brianf at med.uvm.edu
Fri Nov 10 18:47:54 EST 1995

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).

On a Mac you can delete columns in Microsoft word, by holding
down the OPTION key as you select text.  I suspect that this
will not be convientient with PHYLIP files unless you
can convince Word to us a page width that is very wide.

I have access to a program which strips any site in an alignmnet
which contains a gap in any of the sequences.  It is called GapStrip.
I will check into it on Monday and see where we got it.
It is a UNIX program.

MASE (multiple alignment sequence editor) is shareware or freeware
and does a good job, but not automatically.  I can also look up
where to get this, or you could search the WWW for it.

: Many thanks

: Jeremy

*  Brian Foley               *  btf at t10.lanl.gov                   *
*  T-10, MS-K710, LANL       *  http://hiv-web.lanl.gov            *
*  Los Alamos, NM 87545 USA  *  http://www.uvm.edu/~bfoley         *

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