Difference between revisions of "Applications/iqtree"

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==Application Details==
 
==Application Details==
*A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
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*Description: Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) a very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
*Version: MPI AVX 8.2.11
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*Version: MPI 1.4.4
*Licence: Open source
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*Licence: Open source
  
 
==usage==
 
==usage==
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Below is how to submit the same example using our scheduler slurm.
 
Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
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please replace /home/USERNAME/PATH/OF/DIR with the path of the directory where you copied the example.phy file or to the file that you want to use.
 
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
 
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
 
#!/bin/bash
 
#!/bin/bash
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#SBATCH --exclusive        # Request exclusive access to a node (all 28 cores, 128GB of RAM)
 
#SBATCH --exclusive        # Request exclusive access to a node (all 28 cores, 128GB of RAM)
  
module load openmpi/gcc/1.10.2
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module add openmpi/gcc/1.10.2
 
cd /home/USERNAME/PATH/OF/DIR
 
cd /home/USERNAME/PATH/OF/DIR
 
mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
 
mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
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</pre>
 
</pre>
  
==Further Information==
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==Next Steps==
  
 
* http://www.iqtree.org/doc/
 
* http://www.iqtree.org/doc/
  
 
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{{Modulepagenav}}
 
 
{|
 
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
|style="width:95%; border-width: 0" |
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]]
 
* [[General|General]]
 
* [[Training|Training]]
 
* [[Programming|Programming support]]
 
|-
 
|}
 

Latest revision as of 10:48, 16 November 2022

Application Details

  • Description: Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) a very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
  • Version: MPI 1.4.4
  • Licence: Open source

usage

Interactive

While logged into viper login node: you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
 

Batch Session

Below is how to submit the same example using our scheduler slurm. please replace /home/USERNAME/PATH/OF/DIR with the path of the directory where you copied the example.phy file or to the file that you want to use.

#!/bin/bash
#SBATCH -J IQtree_example   # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -n 14               # number of cores
#SBATCH -N 1                # Number of nodes
#SBATCH -p highmem          # Slurm partition, where you want the job to be queued
#SBATCH --exclusive         # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module add openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy


Then the next step is to submit the above script to slurm for example if you name the above text file iqtree.sh


[user@login01 ~]$ sbatch iqtree.sh
Submitted batch job 409671

Next Steps





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