== IQ-TREE ==

Load procedure: `module load iqtree`

The software and instructions can be found on: http://www.iqtree.org/


=== Mykopat Grid specifics ===
None

=== Installed versions ===
* 1.6.12 (called by iqtree)
* 2.1.3 (called by iqtree2)


QUIRK NOTE FOR PARTITIONED ALIGNMENTS: if you have a RAXML-type .txt file specifying where partitions begin and end want to build a tree, you have to let iqtree determine those partitions for you and use the resultant XXXbest_scheme.nex file as input for "real" tree building. It doesn't correctly recognize models in RAXML-type partition files for treebuilding.

ex. start with something like:
iqtree2 -s sequences.phy -p raxml_type_partitionsfile.txt  -ntmax 10 -T AUTO -m TESTMERGEONLY

followed by:
iqtree2 -s sequences.phy -p raxml_type_partitionsfile.txt.best_scheme.nex ...

-GP