Difference between revisions of "IGTP"

Latest revision as of 19:06, 12 August 2022

Description

iGTP is a program designed to help biologists infer species phylogenies from gene phylogenies, using the gene tree parsimony (GTP) approach. The program implements efficient heuristics which allows it to handle large-scale species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs.

iGTP provides the following features:

* Allowing unrooted input gene trees
* Providing three-dimensional tree visualization
* Computing reconciliation costs

Environment Modules

Run module spider iGTP to find out what environment modules are available for this application.

System Variables

HPC_IGTP_DIR - installation directory
HPC_IGTP_BIN

Citation

If you publish research that uses iGTP you have to cite it as follows: Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein, "iGTP: A software package for large-scale gene tree parsimony analysis", BMC Bioinformatics 2010, 11:574.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|iGTP}}
@@ Line 31: / Line 31: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-<!--===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN
+* HPC_{{uc:{{#var:app}}}}_BIN
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==