Does a called locus mean it recombined?

No. A locus that evolves at a different rate, or with different rate variation among sites, is rejected too. Treat a called locus as a candidate for comparing its tree with the others.

Why are all my p-values 0.01?

With 99 permutations the smallest p is 1/100. Raise the number of permutations to tell strong conflicts apart.

Is anything uploaded?

No. Every search runs in the browser on the records in your project.

Analyze

Gene incongruence: which loci of a multi-locus alignment have a different history

Ask which loci of a multi-locus alignment have a different history from the rest. For every locus, the test counts how many extra parsimony steps it costs to force that locus onto the same tree as the others, and compares that cost with random deals of the same columns into loci of the same sizes. One test covers every locus at once, one tests each locus against the others, and the false discovery rate is controlled across loci.

Open Gene incongruence: which loci of a multi-locus alignment have a different history Open the Gene incongruence sample

Seven housekeeping genes of 16 Neisseria strains, each tested for whether its tree fits the others’ worse than chance, the signature of a gene with its own history

What it does

01The incongruence length difference of Farris et al.: the extra parsimony steps one shared tree costs over each locus's own tree
02A permutation null that deals the same columns into loci of the same sizes
03One test over every locus at once and one per locus against all the others
04Benjamini–Hochberg or Benjamini–Yekutieli control of the false discovery rate across loci
05A Clopper–Pearson interval on every Monte Carlo p

What it runs on

Every parsimony length a run computes is checked against Bio.Phylo's own NNI search from the same start tree, and the false discovery rate against R. The panel runs on @ports/discover, @ports/workflow.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Does a called locus mean it recombined?: No. A locus that evolves at a different rate, or with different rate variation among sites, is rejected too. Treat a called locus as a candidate for comparing its tree with the others.
Why are all my p-values 0.01?: With 99 permutations the smallest p is 1/100. Raise the number of permutations to tell strong conflicts apart.
Is anything uploaded?: No. Every search runs in the browser on the records in your project.

Also searched as

incongruence length difference test · ILD test · partition homogeneity test · gene tree conflict · recombination between MLST loci · which gene has a different tree · parsimony incongruence test · false discovery rate across loci