Efficient software for phylogenomic inference

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

References:

• B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534.
• L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies Mol. Biol. Evol., 32:268-274.

• iqtree Main Site
• iqtree Github

• Module Name: iqtree (see the modules page for more information)
• Multithreaded application
• Example files in $IQTREE_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=6g -c 8
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load iqtree

[user@cn3144 ~]$ cp $IQTREE_TEST_DATA/* .

[user@cn3144 ~]$ iqtree2 -s example.phy -nt $SLURM_CPUS_PER_TASK
IQ-TREE multicore version 2.1.2 COVID-edition for Linux 64-bit built Oct 22 2020
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    cn0852 (AVX512, FMA3, 377 GB RAM)
Command: iqtree2 -s example.phy -nt 8
Seed:    830607 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Oct 26 10:33:27 2020
Kernel:  AVX+FMA - 8 threads (8 CPU cores detected)

Reading alignment file example.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 17 sequences with 1998 columns, 1152 distinct patterns
1009 parsimony-informative, 303 singleton sites, 686 constant sites
[...]
Total number of iterations: 102
CPU time used for tree search: 34.761 sec (0h:0m:34s)
Wall-clock time used for tree search: 4.757 sec (0h:0m:4s)
Total CPU time used: 44.325 sec (0h:0m:44s)
Total wall-clock time used: 6.151 sec (0h:0m:6s)

Analysis results written to:
  IQ-TREE report:                example.phy.iqtree
  Maximum-likelihood tree:       example.phy.treefile
  Likelihood distances:          example.phy.mldist
  Screen log file:               example.phy.log

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. iqtree.sh). For example:

#!/bin/bash
module load iqtree
iqtree2 -s example.phy -nt $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=6g iqtree.sh

Create a swarmfile (e.g. iqtree.swarm). For example:

iqtree2 -s example1.phy -nt $SLURM_CPUS_PER_TASK
iqtree2 -s example2.phy -nt $SLURM_CPUS_PER_TASK
iqtree2 -s example3.phy -nt $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f iqtree.swarm -g 6 -t 8 --module iqtree