This repository has been archived by the owner on Aug 10, 2022. It is now read-only.

Requirements

Jump to bottom

nyoungb2 edited this page Jan 11, 2014 · 9 revisions

These are the software requirements for running various workflows of CLdb.

Perl modules

BioPerl (tested on v1.006901)
Set::IntervalTree

Database construction

sqlite3 (tested on v3.7.17)

Spacer, direct repeat, and leader clustering

cd-hit-est (tested on v4.6)

Alignments of leader regions

mafft (tested on v7.037b)

Spacer blasting

blast+ toolkit (tested on 2.2.27+)

Plotting loci

R (tested on v3.0.1)
R package: genoPlotR (tested on v0.8)
ITEP (if coloring genes by gene cluster in loci plots)