Applications/iqtree - Revision history

Pysdlb: /* Next Steps */

2022-11-16T10:48:04Z

‎Next Steps

Pysdlb: /* Navigation */

2022-11-16T10:47:57Z

‎Navigation

Pysdlb at 11:50, 15 November 2022

2022-11-15T11:50:42Z

Pysdlb at 13:01, 24 May 2019

2019-05-24T13:01:01Z

Pysdlb at 14:22, 7 June 2018

2018-06-07T14:22:21Z

Seif: /* Application Details */

2017-11-16T17:09:11Z

‎Application Details

Seif: /* Interactive */

2017-11-16T17:04:12Z

‎Interactive

Seif: /* Batch Session */

2017-11-16T17:00:28Z

‎Batch Session

Seif: /* usage */

2017-11-16T16:59:53Z

‎usage

Seif: /* Application Details */

2017-11-16T16:55:22Z

‎Application Details

← Older revision		Revision as of 10:48, 16 November 2022
Line 55:		Line 55:

	* http://www.iqtree.org/doc/		* http://www.iqtree.org/doc/
−

	{{Modulepagenav}}		{{Modulepagenav}}

← Older revision		Revision as of 10:47, 16 November 2022
Line 57:		Line 57:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 1: / Line 1: @@
 ==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) 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.
+*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
@@ Line 25: / Line 25: @@
 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.
+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;">
 #!/bin/bash
@@ Line 52: / Line 52: @@
 </pre>
-==Further Information==
+==Next Steps==
 * http://www.iqtree.org/doc/

@@ Line 57: / Line 57: @@
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 36: / Line 36: @@
 #SBATCH --exclusive         # Request exclusive access to a node (all 28 cores, 128GB of RAM)
-module load openmpi/gcc/1.10.2
+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

@@ Line 17: / Line 17: @@
 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 ~]$ /trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause
+[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
 </pre>
@@ Line 37: / Line 38: @@
 module load openmpi/gcc/1.10.2
 cd /home/USERNAME/PATH/OF/DIR
-/trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause
+mpirun  /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
 </pre>
 Then the next step is to submit the above script to slurm
-for example if you name the above text file raxml.sh
+for example if you name the above text file iqtree.sh
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[user@login01 ~]$ sbatch raxml.sh
+[user@login01 ~]$ sbatch iqtree.sh
 Submitted batch job 409671