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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