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Which is the MULTIPLE ALIGNMENT code that can be INTERFACED most EASILY ?

Francois Jeanmougin pingouin at chouchen.u-strasbg.fr
Thu Jul 31 01:54:54 EST 1997

In article <EE5HqK.3yE at hermes.hrz.uni-bielefeld.de>,
	fuellen@ REPLY-TO_HEADER_HAS_BEEN_SET_IN_ORIGINAL_POST_OR_JUST_REMOVE_THIS_SPAM_BLOCKER techfak.uni-bielefeld.de (Georg Fuellen) writes:
> I'm eager to hear your experiences and advice regarding multiple alignment 
> software, and interfacing to it. Just reply straight away, do it now :)
> E.g., would you recommand ClustalW / MSA ? Or MAP ? Or MultAlin ? 
> Any other tools you tried ?
> Do you have unreleased code for the task ?

	You know what? ... I think this will begin to be a joke.. But
everytime someone talk about multiple alignment programme, I'm coming
with Clustal. Anyway, most of the packages I know (seqpup, GCG8 and GCG9,
others, but I don't want to say something wrong) are interfacing easily
ClustalW. This for two reasons :
	- ClustalW can be driven with command-line parameters so that it
can be launched as a child process without effort (that's what is done 
with seqlab or wpi).
	- The algorithm and the interface are independant (it is the same
algorithm for CLustalW and ClustalX) and so you can try to use the code
(for non-commercial applications and after asking to Julie Toby and Des,
of course).

	Julie is on hollidays at the moment, so I can't go in details.

	Feel free to contact if you have any question.


P.S.: Remember taht ClustalX provide some analysis tools that can't be used
by ClustalW and so ClustalX is more powerfull. But you can interface 
ClustalX easily also...
P.P.S.: To All: Remember that we updated ClustalW1.7 with several algorithm
improvement, please update your files...
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
"Ce sont des désespoirs d'intellectuels ennuyés, ou des ennuis 
d'intellectuels désespérés, comme vous voulez, comme vous voulez" M. Benin

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