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