Custom *set* of initial trees from file

[ear...@gmail.com]

Hello everyone,

I would like to do a tree search providing my own set of initial trees, but it looks like IQTree is just using the first tree in the tree file that I pass with the `-t` option. I am testing with a Newick file with 10 trees; later there would be hundreds.

I am calling IQTree from a script like this:

`iqtree2 -m $substitution_model -s $aln_path -seed $iqtree_seed --runs 1 -nt 2 -pre $iqtree_pre_string -t $init_pool_path --quiet`

The log file says "Do NNI search on 1 best initial trees", whereas a regular tree search without `-t` says "Do NNI search on 20 best initial trees". I tried setting `-ninit` and `-ntop` as well, to no avail.

Is there a way to make IQTree accept all my initial trees?

Cheers,

Eduardo