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Re: Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package


  Here are some comments about the description (done with my wife who
works as biologist with such kind of software).

Charles Plessy wrote:
 PHYLIP (the PHYLogeny Inference Package) is a package of programs for
 inferring phylogenies (evolutionary trees). Methods that are available
 in the package include parsimony, distance matrix, and likelihood
 methods, including bootstrapping and consensus trees. Data types that
 can be handled include molecular sequences, gene frequencies,
 restriction sites and fragments, distance matrices, and discrete
 EMBASSY packages include applications with the same look and feel as
 EMBOSS applications, but which the author wishes to be kept separate
 from EMBOSS. This is usually because the packages are for specialised
 sequence analysis or for non-sequence based anaylsis, or are licensed
 differently to EMBOSS (i.e. non GPL).
 EMBOSS - the European Molecular Biology Open Software Suite - is an
 analysis package specially developed for the needs of the molecular
 biology user community.
 The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them
 from the original programs.

EMBOSS should be presented before EMBASSY as EMBASSY use EMBOSS in its
And we fail to see the relation between EMBOSS and PHYLIP. Does PHYLIP
is a part of EMBOSS ?

Moreover, reading your part on EMBASSY, I understand that EMBOSS is GPL
but not necessarily EMBASSY. Am I right ? (I cannot because PHYLIP is not
free, so either PHYLIP is not a part of EMBOSS or EMBOSS is not all GPL)

Perhaps, you can keep the first paragraph about PHYLIP and then add
something such as:
Original PHYLIP software is not free. EMBASSY PHYLIP is a free rewrite
in the context of the EMBOSS (European Molecular Biology Open Software
Suite) project. The EMBASSY PHYLIP programs all have the prefix "f" to
distinguish them from the original programs.

[of course, I can be totaly wrong if I did not understand the relations

  Best regards,

Vincent Danjean                 Adresse: Laboratoire d'Informatique de Grenoble
Téléphone:  +33 4 76 61 20 11            ENSIMAG - antenne de Montbonnot
Fax:        +33 4 76 61 20 99            ZIRST 51, avenue Jean Kuntzmann
Email: Vincent.Danjean@imag.fr           38330 Montbonnot Saint Martin

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