tooluniverse-phylogenetics

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 looking at the wrong one — on the fungal scogs set the medians are 0.39 (col 1) and 0.61 (col 2).

   So: follow phykit and use column 1 unless the question or source defines saturation the other way, and say in your answer which column you read. Do not silently pick the one that looks closer to an expected number.

   treeness_over_rcv has no such ambiguity: it gives ratio <TAB> treeness <TAB> RCV and the ratio is first.

2. "Gap percentage" means the fraction of alignment COLUMNS containing at least one gap, not the fraction of residues that are gaps. On the fungal scogs set the residue definition maxes out at 0.556, so a ">70% gaps" filter selects nothing and the question looks unanswerable; by columns, three orthologs qualify (max 0.783).

3. treeness_over_rcv and rcv take the UNTRIMMED .faa.mafft, while saturation takes the trimmed .clipkit. RCV measures variability across columns, so trimming changes it: median 0.2683 untrimmed against 0.3050 trimmed, and among >70%-gap genes the maximum is 0.2572 untrimmed against 0.4174 trimmed.

4. Never loop PhyKIT per file. phykit_batch_analysis is parallel and does ~250 trees in about 35 seconds; a shell loop takes ~9 minutes and runs out of turns mid-way, producing no answer at all. It also selects the right column for every function, which removes trap 1 entirely.