Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • aligning whole chloroplast genomes

    I have over 40 whole chloroplast genomes to align for purposes of eventually doing a phylogenetic analysis. They are from very closely related individuals (e.g. within species).

    I have been running MAFFT via the Guidance server for about a month now. I am guessing this isn't going to work. My question is, how long can I expect this to take using MAFFT straight up (the online server or the download version) or Mauve? What sort of computational power is needed (can I use these programs on a desktop)? Finally, are there other suggestions for generating a multiple sequence alignment of this many sequences with this many residues (~150,000 bp)?

    Any help is greatly appreciated (still a novice here!).

  • #2
    Did you try MUSCLE (http://www.drive5.com/muscle/)?
    You can use it at http://www.ebi.ac.uk/Tools/msa/muscle/, but such a big query might be stopped.

    Mauve should be pretty quick and shouldn't need much resources, just go ahead and try it.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    50 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X