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tooluniverse-phylogenetics

Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT), parsimony-informative sites, alignment gap analysis, DVMC, long-branch detection, BUSCO orthologs. Uses PhyKIT, Biopython, DendroPy. Use to align a set of sequences, build a tree from sequences or an alignment, or for phylogenetic tree QC, multi-gene phylogenomics, evolutionary-rate analysis, and comparative-genomics studies.

plugin/skills/tooluniverse-phylogenetics/SKILL.md

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# Phylogenetics and Sequence Analysis

## Four traps that produce a confidently wrong number

Each of these was observed producing a wrong answer *while the correct guidance
was already present further down this file*. Check them before you answer.

1. **PhyKIT prints more than one column, and for `saturation` the two
   conventions disagree — state which you used.** `phykit saturation` prints
   `saturation <TAB> |saturation-1|`. Its own `--help` is explicit: *"The first
   value is the saturation value and the second column is the absolute value of
   saturation minus 1."* But several published analyses (and some reference
   answers derived from them) report the **second** column as "the saturation
   value". The two always sum to 1.0000, which is the tell that you may be