Dear Prof. Aaron Darling and Mauve users,
I'm writing to you to ask some questions about the use of
progressiveMauve.
The topic of my work is to do a whole genome phylogeny and analyze (by
ClonalOrigin) the recombination fluxes on a set of 27 whole genome
sequences of bacteria, but most of them consist of contigs, since they
are still in draft form. So I have installed Mauve in my linux64 server
and I'm trying to launch progressiveMauve on 27 multifasta file.
So the my first question is: Does progressiveMauve works fine on genome
consisting of contigs? or Should I create a concatenamer of contigs in
order to obtain only 27 fasta sequences?
Then most of my genome sequences contain sequence/contigs annotated as
plasmid. About this do you think it is better to run the
progressiveMauve on chromosomes and on plasmids separately? Which is
your experience?
Actually I have already obtained a core_alignment.xmfa (LCB greater than
100) from my first attempt of running, and now I'm waiting for the
result of Clonalframe (ClonalFrame -x 10000 -y 10000 -z 10
core_alignment.xmfa core_clonalframe.out.1 > cf_stdout.1 &...)
I have launched the jobs 7 days ago but it is still running, so Is it
normal that this job take so many time? How I could speed up this job?
Thanks if you have the possibility to answer to these my several
questions.
Best regards
Dott.ssa Annalisa Giampetruzzi
Dott.ssa Annalisa Giampetruzzi
Università degli Studi di Bari Aldo Moro
Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti
Di.S.S.P.A.
Via Amendola 165/A 70126 BARI
tel. 0805442538
fax. 0805443608
annalisa.giampetru...@uniba.it
annalis...@hotmail.it
skype giampe79
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