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Table 4. List of programs and parameters in the VMGAP

From: The Viral MetaGenome Annotation Pipeline (VMGAP): An automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

Pipeline job name

Program

Parameters

A CLAME_HMM

hmmpfam

E 0.001

A CLAME_PEP

Blastp

b 50 -e 1e-5

ALLGROUP_PEP

Blastp

b 50 -e 1e-5

CDD_RPS

Rpsblast

b 50 -e 1e-3

ENV_NR

blastp

b 50 -e 1e-3

ENV_NT

tblastn

b 50 -e 1e-3

FRAG_HMM

hmmpfam

E 0.001

PEPSTATS

Pepstats

None

PFAM/TIGRFAM_HMM

Hmmpfam

E 0.001

PRIAM

Priam

e 1e-10

SANGER_PEP

Blastp

b 50 -e 1e-5

SIGNALP

Signalp

tgram- -trunc 70

TMHMM

tmhmm

None