Difference between revisions of "PanX"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
Latest revision as of 21:22, 6 December 2019
Description
panX is a software package for pan-genome analysis, interactive visualization and exploration. The analysis pipeline is based on DIAMOND (Buchfink et al. 2015 Nature Methods), MCL and phylogeny-aware post-processing, which takes a set of annotated bacterial strains as input (e.g. NCBI RefSeq records or user's own data in GenBank format). Alls genes from all strains are compared to each other via the fast protein alignment tool DIAMOND and then clustered into orthologous groups using MCL and adaptive phylogenetic post-processing, which split distantly related genes and paralogs if necessary. For each gene cluster, corresponding alignment and phylogeny are constructed. All core gene SNPs are then used to build strain/species phylogeny.
Environment Modules
Run module spider panx to find out what environment modules are available for this application.
System Variables
- HPC_PANX_DIR - installation directory
- HPC_PANX_BIN - executable directory