EMBOSS 1.12.0

[David Martin]

On Tue, 17 Apr 2001 ableasby at hgmp.mrc.ac.uk wrote:

>
> EMBOSS 1.12.0 contains the following new programs in addition to
> the usual load of library mods/fixes/etc.
>
> Distmat: Creates a distance matrix from multiple alignments of nucleotide or
> protein sequences. The sequences need to be aligned before running
> this program. The quality of the alignment is of paramount importance
> in obtaining meaningful information from this analysis.

This looks interesting. Could I suggest some refinements?

1. Add the sequence count to the top of the output.

2. Substituttion matrices for proteins.

Can this matrix file be read in again by an EMBOSS library routine to
reconstruct the matrix without having to write a new parser? I might be
tempted to write an additivity/ultrametry checker.

> Charge: Simple sliding window plot of charge vs position in a protein
> sequence.
>
> Cai: Codon adaptive index calculation. A measurement of the level of
> usage of the 64 codons in a sequence.
>

And again, every application has absolutely no trace information in the
output such as date and time it was run, by whom, and with which
datafiles/parameters. Is there a way to get a full list of parameters
used in an EMBOSS application (ie everything that could be specified on
the command line..


..d