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  • mm.perrineau
    Member
    • Sep 2012
    • 12
    #1

    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 !!!!
    Tags: snps, tree
    • khoa128
      Junior Member
      • Sep 2012
      • 2
      #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:[email protected]_35Days.EXE

        Comment

        • AdrianP
          Senior Member
          • Apr 2011
          • 130
          #3
          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:

          Giant alignment, high identity, which model for phylogeny? - SEQanswers
          http://seqanswers.com/forums/showthread.php?p=112840
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

            Comment

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