(no subject)

Arnaud Chatonnet chatonne at ensam.inra.fr
Thu Feb 12 08:27:57 EST 1998

I use MAKEINF from Arend Sidow
in the phylip package
MAKEINF (for "MAKE INFile") reads an amino acid or nucleic acid
alignment of the format of Jotun Hein's ALIGN program (MBE 1989,
6:649-668) and then outputs an aligned set of nucleic acid sequences in
the sequential format used by the PHYLIP package. Please note that if
you don't use ALIGN, you can easily edit your alignments so that they
can be used with MAKEINF.

It is particularly useful for the analysis of protein-coding genes at
the nucleic acid level. It may also be used on nucleic acid sequences
which do not encode proteins. I wrote it because I analyze first plus
second position changes which result in amino acid replacements.
Editing such sequences can be extremely time-consuming when it is done
by hand.

a) Given an alignment, MAKEINF puts the gaps in the right places by
using the alignment (usually an amino acid alignment, but nucleic acids
are ok as well) as a template on which to align the corresponding
nucleic acid sequences. The resulting output file is directly PHYLIP-

----------sans accents pour etre lu par tout le monde-------------------
Arnaud Chatonnet
Departement de physiologie animale               Tel (33) 04 99 61 26 77
Institut National de la Recherche Agronomique    Fax (33) 04 67 54 56 94
place Viala 34060 Montpellier cedex1 FRANCE      
E mail chatonne at ensam.inra.fr

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