IQTree

IQ TREE on XSEDE

IQ-TREE was designed to address “deep phylogenetic” questions in the tree of life. Here we offer IQ-TREE on XSEDE resources, which will make the analysis run as fast as possible.

IQ-TREE software has a strong emphasis on phylogenomic inference. The IQ-TREE team goals are:

    Accuracy: Proposing novel computational methods that perform better than existing approaches.
    Speed: Allowing fast analysis on big data sets and utilizing high performance computing platforms.
    Flexibility: Facilitating the inclusion of new (phylogenomic) models and sequence data types.
    Versatility: Implementing a broad range of commonly-used maximum likelihood analyses.

The name IQ-TREE comes from the fact that it is the successor of IQPNNI and TREE-PUZZLE software.

IQ-TREE Documentation here.

 

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names	Sample File from a Test
input file	iq_tree.infile.phy
partition file	iq_tree.partition.nex
Sample Output File Type	File Name
log file	iq_tree.output.log
tree file	iq_tree.output.treefile
distance matrix	iq_tree.output.mldist
neighbor joining tree	iq_tree.output.bionj
checkpoint file	iq_tree.output.ckp.gz

In good practice, one conducts multiple runs of the IQ-TREE program, combines the results, and analyzes them. At present, CIPRES does not support the restart function for IQ Tree. We hope to have this feature in place by Jan 31, 2017.

If you use IQ-TREE here, please cite:

L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32:268-274. DOI: 10.1093/molbev/msu30

If there is a tool or a feature you need, please let us know.