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Accepted Softwares - To publish Data (Nov/04/2006 )

hello,
i have just started getting genotype information for one of the virus that i will be concentrating on for my phd thesis, it will be to do a molecular epidemiology based study of the virus and will involve lots of sequencing and analysis of the data with others from the ncbi.
i will have to check for the homology and also create trees for these as well as look in for new consensus sequence.
the problem i am facing is the availability of so many analysis programs, i do not know which are the programs that are accepted by the journals and in general other scientific communities around the world. i would liek to have a list of these programs that are acceptable in the scientific community so that i can choose the program i am comfortable with and then use it.

thekid.

p.s: i don't want to end up analysisng my data and at a international level symposium get the comment that the program i have used is not good and the result has to be rechecked with some other programme.

-thekid-

For alignment check this paper

Serafim Batzoglou
The many faces of sequence alignment
BRIEFINGS IN BIOINFORMATICS. VOL 6. NO 1. 6–22. MARCH 2005

-djv0022-

whatever program you use, someone will have a problem with it...it's the way the field works... who was that said... 'if you can find something that everyone agrees on, it's wrong'?

-perlmunky-

QUOTE (perlmunky @ Nov 6 2006, 01:57 PM)
whatever program you use, someone will have a problem with it...it's the way the field works... who was that said... 'if you can find something that everyone agrees on, it's wrong'?


I agree, most important is, that you are allowed to use an analysis method /calculation for your available data type. There are some programs and approaches everyone knows (e.g. Paup, Reap, Phylip, Clustal, Mega; AMOVA, similarity -distance calculations, different tree calc methods.....) and some very special you may have to explain in detail, but if you say e.g.: I have sequence data and analyzed them with a common alignment/distance method (independed from program) normally nobody will ask further.

-hobglobin-