Bespoke tree <-> OT 16 incompatibilities

[lentinj]

The bespoke tree expects snippets that aren't there:

WARNING:root:Could not find the following taxa: 4795972, 5205266, 818997, 978560, 356644, 471706, 29488, 29492, 406376, 956134

These are either Sharks or Rotifers:

• https://www.onezoom.org/life/@=4795972
• https://www.onezoom.org/life/@=5205266
• https://www.onezoom.org/life/@=818997
• https://www.onezoom.org/life/@=978560
• https://www.onezoom.org/life/@=356644
• https://www.onezoom.org/life/@=471706
• https://www.onezoom.org/life/@=29488
• https://www.onezoom.org/life/@=29492
• https://www.onezoom.org/life/@=406376
• https://www.onezoom.org/life/@=956134

[lentinj]

NB: Since switching to the dated tree Aenigmarchaeota_ott4795972@, Diapherotrites_ott5205266@ are now found. The rest are still missing though:

[2026-06-09 16:37:47,644] No subtree found for Rotifera_ott471706@
[2026-06-09 16:37:47,644] No subtree found for Chimaera_ott29488@
[2026-06-09 16:37:47,644] No subtree found for Hydrolagus_ott29492@
[2026-06-09 16:37:47,644] No subtree found for Rajidae_ott978560@
[2026-06-09 16:37:47,644] No subtree found for Arhynchobatidae_ott406376@
[2026-06-09 16:37:47,644] No subtree found for Rhiniformes2__ott356644~-456585-356651-1041304@
[2026-06-09 16:37:47,644] No subtree found for Narcinidae_ott818997@
[2026-06-09 16:37:47,644] No subtree found for Squaliolus_ott956134@

[lentinj]

median_PD_shark_tree.txt sourced from: https://vertlife.org/data/sharks/ and https://www.nature.com/articles/s41559-017-0448-4

my method (for records) - read in the distribution of 10,000 trees, calculate phylogenetic diversity of each, find out which tree yields the median value, interpret this as a median tree to move forward wit, output as newick:

rm(list=ls())

# install useful packages
require('ape')
require('caper')

# Read all trees
trees <- ape::read.tree(file='Chond.10Cal.10kTreeSet.tre')

# Calculate PD for each tree
pd <- sapply(trees, function(tr) sum(tr$edge.length))

# Median PD value
median_pd <- median(pd)

# Tree closest to the median
median_idx <- which.min(abs(pd - median_pd))
median_tree <- trees[[median_idx]]

# Newick string
newick <- write.tree(median_tree)
writeLines(newick, "median_PD_shark_tree.txt")