Changes between Version 7 and Version 8 of Software/IQ-TREE

Timestamp:

Oct 6, 2022, 5:47:54 PM (2 years ago)

Author:

grpo0001

Comment:

adding partitioned alignment quirk note

Software/IQ-TREE

@@ -4 +4 @@
 
 The software and instructions can be found on: http://www.iqtree.org/
+
 
 === Mykopat Grid specifics ===
@@ -11 +12 @@
 * 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