Program for aligning coding sequences?

Chatonnet chatonne at ensam.inra.fr
Mon Oct 26 11:16:27 EST 1998


> There is MAKEINF

MAKEINF (for "MAKE INFile") reads an amino acid or nucleic acidalignment 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.

WHEN do I want to use this program?

It is particularly useful for the analysis of protein-coding genes at
the nucleic acid level.

> Does anyone know of an alignment program which takes into account the fact
> that the input file contains protein-encoding nucleotide sequences? In other
> words some programs where the nucleotide alignment is guided by the amino
> acid alignment (nucleotide gaps are inserted in multiples of three etc.).
>
> Frank



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