Table_dependency_version.txt

Basic requirement:
Python : version higher or equal to 3.4.
BioPython: version higher or equal to 1.65.
Wget: version higher or equal to 1.17.1.
Matplotlib : version higher or equal to 1.5.0.

Annotation transfer:
BioPerl: version higher or equal to 1.6.1.
RATT : version higher or equal to 1.64.

SNP calling:
Samtools : version higher or equal to 1.3.1 (using htslib 1.3.1).
Bcftools : version higher or equal to 1.3.1 (using htslib 1.3.1).

TSS and PS prediction:
TSSpredator : version higher or equal to 1.06.

TSS and PS parameter optimization:
TSSpredator : version higher or equal to 1.06.

sRNA detection:
Blast+ : version higher or equal to 2.2.28+.
ViennaRNA : version higher or equal to 2.3.2. RNAfold, mountain.pl and relplot.pl are needed for sRNA prediction.

Terminator detection:
TranstermHP : version higher or equal to 2.09.
ViennaRNA : version higher or equal to 2.3.2. RNAfold is needed for terminator prediction.

Promoter search:
MEME : version higher or equal to 4.11.1.
GLAM2 : version higher or equal to 4.11.1.
MPICH : version higher or equal to 3.2. It is for parallel version of promoter detection.

sRNA target prediction:
ViennaRNA : version higher or equal to 2.3.2.
RNAup, RNAplex, RNAplfold are required for executing many modules of ANNOgesic.
IntaRNA: version higher or equal to 2.0.4.

Circular RNA detection:
Samtools : version higher or equal to 1.3.1 (using htslib 1.3.1).
Segemehl : version higher or equal to 0.1.9.

Riboswitch and RNA thermometer identification:
Infernal : version higher or equal to 1.1.1.

CRISPR detection:
CRT: version higher or equal to 1.2.

Subcellular localization prediction:
Psortb : version higher or equal to 3.0.

Protein-protein interaction detection:
Networkx : version higher or equal to 1.10.

Generating screenshots of IGV:
IGV : version higher or equal to 2.3.20.

Colorization of screenshots:
ImageMagick : version higher or equal to 6.9.0-0.