I will be crazy: Help about SNPs and tree!!!!

mm.perrineau · 01-17-2013, 11:14 AM

Hi,

Somebody can help me????
I will be crazy: I am not bioinformaticien and i have to make a phylogenetic tree reflecting the genetic distance between 4 strains...
I have one strain well sequenced and his genome is annotated...
I have all reads mapped on this genome for the 3 others strains...

I used CLC for the SNPs calling and now i am stopped since few weeks and i become crazy!!!!!!!!
I need to build a simple tree reflecting the genetic distance between those 4 strains...
Can you help me...

And i need too some software to make some statistical tests on the SNPs... Do i have some genomic regions ? some genes under selection pressure ?

Thank you very much !!!!!

And please help me i am totally desperate !!!!

khoa128 · 06-14-2013, 08:39 PM

Hi
you to be used software of this: NextGENe® software for Next Generation (NGS) Sequence Analysis. You may download a 30 day trial from our ftp site:

ftp://ngval:YP5NM7SZ@ftp.softgenetic...ion_35Days.EXE

AdrianP · 08-07-2013, 09:42 AM

Hello,

I do not mean to advertise my own thread, but it seems like we are doing something similar. Check out what I have done so far and my obstacles:

http://seqanswers.com/forums/showthread.php?p=112840

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01-17-2013, 11:14 AM	#1
mm.perrineau Member Location: New Jersey Join Date: Sep 2012 Posts: 12	I will be crazy: Help about SNPs and tree!!!! Hi, Somebody can help me???? I will be crazy: I am not bioinformaticien and i have to make a phylogenetic tree reflecting the genetic distance between 4 strains... I have one strain well sequenced and his genome is annotated... I have all reads mapped on this genome for the 3 others strains... I used CLC for the SNPs calling and now i am stopped since few weeks and i become crazy!!!!!!!! I need to build a simple tree reflecting the genetic distance between those 4 strains... Can you help me... And i need too some software to make some statistical tests on the SNPs... Do i have some genomic regions ? some genes under selection pressure ? Thank you very much !!!!! And please help me i am totally desperate !!!!

06-14-2013, 08:39 PM	#2
khoa128 Junior Member Location: hanoi Join Date: Sep 2012 Posts: 2	Hi you to be used software of this: NextGENe® software for Next Generation (NGS) Sequence Analysis. You may download a 30 day trial from our ftp site: ftp://ngval:YP5NM7SZ@ftp.softgenetic...ion_35Days.EXE

08-07-2013, 09:42 AM	#3
AdrianP Senior Member Location: Ottawa Join Date: Apr 2011 Posts: 130	Hello, I do not mean to advertise my own thread, but it seems like we are doing something similar. Check out what I have done so far and my obstacles: http://seqanswers.com/forums/showthread.php?p=112840