Difference between revisions of "SEPP"

Latest revision as of 20:39, 12 August 2022

Description

SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

Environment Modules

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

System Variables

HPC_SEPP_DIR - installation directory
HPC_SEPP_BIN - executable directory
HPC_SEPP_CONF - configuration examples directory

Additional Information

The sepp module includes all three components of the SEPP suite - SEPP, TIPP, and UPP - the three methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem..

SEPP - SATe-enabled phylogenetic placement
TIPP - Taxonomic identification and phylogenetic profiling
UPP - Ultra-large alignments using Phylogeny-aware Profiles

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|sepp}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
+* HPC_{{uc:{{#var:app}}}}_CONF - configuration examples directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 42: / Line 34: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+The sepp module includes all three components of the SEPP suite - SEPP, TIPP, and UPP - the three methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem..
+* SEPP - SATe-enabled phylogenetic placement
+* TIPP - Taxonomic identification and phylogenetic profiling
+* UPP - Ultra-large alignments using Phylogeny-aware Profiles
 |}}
 <!--PBS scripts-->