Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • phylogenetic analysis with stacks using RAD-seq

    Hi all,

    I am trying to do phylogenetic analysis using Stacks --phylip option it says no data to write in phylip

    Generating nucleotide-level summary statistics for population '1'
    Population '1' contained 0 incompatible loci -- more than two alleles present.
    Generating nucleotide-level summary statistics for population '2'
    Population '2' contained 0 incompatible loci -- more than two alleles present.
    Tallying loci across populations...done.
    Pruned 264 variant sites due to filter constraints (too many alleles or too few samples at a site, MAF too low, or heterozygosity too high).
    Removing 253 additional loci for which all variant sites were filtered... retained 2785 loci.
    Regenerating nucleotide-level summary statistics for population '1'
    Population '1' contained 0 incompatible loci -- more than two alleles present.
    Regenerating nucleotide-level summary statistics for population '2'
    Population '2' contained 0 incompatible loci -- more than two alleles present.
    Re-tallying loci across populations...done.
    Generating haplotype-level summary statistics for population '1'
    Generating haplotype-level summary statistics for population '2'
    Writing 2785 loci to summary statistics file, './trial/batch_1.sumstats.tsv'
    Writing 2785 loci to observed haplotype file, './trial/batch_1.haplotypes.tsv'
    Writing population data to Phylip file './trial/batch_1.phylip'; logging nucleotide positions to './trial/batch_1.phylip.log'... No data is available to write to the Phylip file.

    Please help

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
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 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