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
--
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* 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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