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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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Output invariant sites position when running +ASC models #328

Closed xiekunwhy closed 3 weeks ago

xiekunwhy commented 1 month ago

Hi,

iqtree auto delete invariant sites when running +ASC models, could you please output a file to tell us which site has been deleted?

By the way, how iqtree define "invariant site" ? We filter snps in vcf using maf ( keep which maf >= 0.05 for example), so I think all sites kept after filtering are variant sites, but iqtree still delete a lot of sites but don't tell me which site has been deleted.

Best, Kun

thomaskf commented 1 month ago

Hi Kun,

To check the details for each site, you can use the -alninfo option. This will generate a .alninfo file, which contains information for every alignment position.

"invariant site" includes three types:

  1. Constant sites
  2. Constant sites with ambiguous characters
  3. Sites with all gaps

Thomas