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