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Table 5 Resources currently defined in BCJ

From: Bioinformatics process management: information flow via a computational journal

Suite/Class Resource Definitions
Sequence search and alignment SimpleBlastall, blastn, blastp, ClustalW, extractSequences
HMMER (biosequence analysis using hidden Markov models) hmmAlign, hmmBuild, hmmCalibrate, hmmSearch, hmmit, hmmer2sam
GROMACS (a molecular dynamics package) editconf, genbox, grompp, mdrun, pdb2gmx
GLIMMER (a system for finding genes in microbial DNA) glimmer
GrailEXP (predicts exons, genes, repeats, and CpG islands) grailAlign, grailCPG, grailExon, grailGeneAssembly, grailRepeats
EMBOSS (The European Molecular Biology Open Software Suite) backtranseq, banana, bl2seq, btwisted, cai, chips, codcmp, coderet, compseq, cpgreport, distmat, einverted, equicktandem, fuzznuc, garnier, geecee, iep, marscan, msbar, newcoils, newcpgseek, octanol, palindrome, pepcoil, pepinfo, pepstats, primersearch, profit, prophecy, prophet, recoder, redata, shuffleseq, silent, water