
%pipein = (
	rnafold_struct => {
		rnaeval => [
			seqstruct,
		],
	},
	sam_model => {
		sampleseqs => [
			model_file,
		],
		align2model => [
			model_file,
		],
		hmmscore => [
			model_file,
		],
		sam2hmmer => [
			model_file,
		],
		buildmodel => [
			model_file,
		],
	},
	phylip_dist => {
		bionj => [
			infile,
		],
		weighbor => [
			infile,
		],
		pyramids => [
			infile,
		],
		kitsch => [
			infile,
		],
		fitch => [
			infile,
		],
		quicktree => [
			distfile,
		],
		neighbor => [
			infile,
		],
		distquart => [
			distfile,
		],
		njdist => [
			distances,
		],
	},
	consensus_matrix => {
		patser => [
			matrix,
		],
	},
	seqsfile => {
		polydot => [
			sequences,
		],
		dialign2 => [
			sequence,
		],
		fuzznuc => [
			sequence,
		],
		listor => [
			firstset,
		],
		dreg => [
			sequence,
		],
		checktrans => [
			sequence,
		],
		dan => [
			sequence,
		],
		sirna => [
			sequence,
		],
		consensus => [
			sequence,
		],
		infoalign => [
			sequence,
		],
		rnaga => [
			seqfile,
		],
		comalign => [
			seq,
		],
		supermatcher => [
			asequence,
		],
		twofeat => [
			sequence,
		],
		primersearch => [
			seqall,
		],
		remap => [
			sequence,
		],
		sigcleave => [
			sequence,
		],
		cai => [
			seqall,
		],
		getorf => [
			sequence,
		],
		restover => [
			sequence,
		],
		splitter => [
			sequence,
		],
		water => [
			bsequence,
		],
		nthseq => [
			sequence,
		],
		restrict => [
			sequence,
		],
		coderet => [
			seqall,
		],
		palindrome => [
			sequence,
		],
		extractfeat => [
			sequence,
		],
		pepcoil => [
			sequence,
		],
		fastasplitter => [
			sequence,
		],
		biosed => [
			sequence,
		],
		prophecy => [
			sequence,
		],
		freak => [
			seqall,
		],
		preg => [
			sequence,
		],
		cpgreport => [
			sequence,
		],
		msbar => [
			sequence,
		],
		marscan => [
			sequence,
		],
		infoseq => [
			sequence,
		],
		tcode => [
			sequence,
		],
		trimest => [
			sequence,
		],
		dca => [
			seq,
		],
		seqmatchall => [
			sequence,
		],
		est2genome => [
			est,
		],
		stssearch => [
			seqall,
		],
		vectorstrip => [
			sequence,
		],
		shuffleseq => [
			sequence,
		],
		geecee => [
			sequence,
		],
		profit => [
			sequence,
		],
		patmatdb => [
			sequence,
		],
		cpgplot => [
			sequence,
		],
		buildmodel => [
			train,
		],
		trimseq => [
			sequence,
		],
		showalign => [
			sequence,
		],
		pepstats => [
			sequence,
		],
		chips => [
			seqall,
		],
		cusp => [
			sequence,
		],
		loadseq => [
			seqfile,
		],
		fuzztran => [
			sequence,
		],
		cons => [
			sequence,
		],
		prophet => [
			sequence,
		],
		showfeat => [
			sequence,
		],
		tmap => [
			sequences,
		],
		garnier => [
			sequencea,
		],
		newcpgseek => [
			sequence,
		],
		sigscan => [
			database,
		],
		compseq => [
			sequence,
		],
		hmoment => [
			seqall,
		],
		helixturnhelix => [
			sequence,
		],
		needle => [
			bsequence,
		],
		pepwindowall => [
			sequences,
		],
		plotcon => [
			sequences,
		],
		emowse => [
			sequence,
		],
		degapseq => [
			sequence,
		],
		transeq => [
			sequence,
		],
		emma => [
			sequence,
		],
		eprimer3 => [
			sequence,
		],
		prettyplot => [
			sequences,
		],
		pscan => [
			sequence,
		],
		revseq => [
			sequence,
		],
		clustalw => [
			infile,
		],
		showseq => [
			sequence,
		],
		tranalign => [
			asequence,
		],
		newcoils => [
			sequence,
		],
		cap3 => [
			seq,
		],
		fuzzpro => [
			sequence,
		],
		tfscan => [
			sequence,
		],
		antigenic => [
			sequence,
		],
		treealign => [
			fileseq,
		],
		hmmalign => [
			seqfile,
		],
		oddcomp => [
			sequence,
		],
		maskfeat => [
			sequence,
		],
		distmat => [
			sequence,
		],
		notseq => [
			sequence,
		],
		charge => [
			seqall,
		],
		predator => [
			seq,
		],
		iep => [
			sequence,
		],
	},
	stamp_trans_file => {
		transform => [
			transfile,
		],
		stamp => [
			listfile,
		],
		sorttrans => [
			scanfile,
		],
	},
	blast_output => {
		seqsblast => [
			infile,
		],
		mview_blast => [
			blast_output,
		],
		mspcrunch => [
			blast_output,
		],
		xblast => [
			blast_output,
		],
		html4blast => [
			input,
		],
	},
	phylip_tree => {
		unroot => [
			treefile,
		],
		seqgen => [
			tree,
		],
		phyml => [
			user_tree_file,
		],
		drawgram => [
			treefile,
		],
		drawtree => [
			treefile,
		],
		consense => [
			infile,
		],
	},
	gb_seq => {
		codnocod => [
			seq,
		],
	},
	hmm_textfile => {
		hmmsearchpar => [
			hmmfile,
		],
		hmmpar => [
			hmmfile,
		],
		hmmer2sam => [
			hmmfile,
		],
	},
	hmmer_HMM => {
		hmmconvert => [
			oldhmmfile,
		],
		hmmsearch => [
			hmmfile,
		],
		hmmalign => [
			hmmfile,
		],
		hmmemit => [
			hmmfile,
		],
		hmmcalibrate => [
			hmmfile,
		],
	},
	pdbfile => {
		CSR => [
			pdbfile,
		],
		homology => [
			pdbfile,
		],
		confmat => [
			pdbfile,
		],
		decorate => [
			pdbfile,
		],
		environ => [
			pdbfile,
		],
		dssp => [
			pdbfile,
		],
		cosa => [
			pdbin,
		],
	},
	gcg_profile => {
		pftools => [
			profile,
		],
	},
	orfs => {
		build_icm => [
			list_orfs,
		],
	},
	stride_outfile => {
		predator => [
			stride_file,
		],
	},
	codonw_coa_file => {
		codonw => [
			cai_file,
		],
	},
	glimmer_orfs_list => {
		glimmer_extract => [
			list_coord,
		],
	},
	pyramid_file => {
		pyreval => [
			pyr_file,
		],
		drawpyr => [
			infile,
		],
	},
	phylip_weights => {
		dnapars => [
			weights_file,
		],
	},
	sam_score => {
		makehist => [
			Nllfile,
		],
	},
	quartfile => {
		qstar => [
			quartfile,
		],
	},
	amps_seqsfile => {
		amps => [
			infile,
		],
	},
	nexus_file => {
		readnexus => [
			seq,
		],
	},
	dssp_outfile => {
		predator => [
			dssp_file,
		],
	},
	psiblast_matrix => {
		blast2 => [
			psi_checkpoint,
		],
		blastpar => [
			psi_checkpoint,
		],
	},
	hmmfile => {
		wise2 => [
			hmmer,
		],
	},
	model => {
		glimmer => [
			models,
		],
	},
	grail_cluster => {
		grailclnt => [
			cluster_file,
			grail2_file,
		],
	},
	stamp_alig_file => {
		dstamp => [
			aligfile,
		],
		avestruc => [
			aligfile,
		],
	},
	stamp_domains_file => {
		pdbseq => [
			domainfile,
		],
		stamp => [
			dbfile,
		],
		pdbc => [
			domains_file,
		],
		alignfit => [
			domainfile,
		],
	},
	consensus_results => {
		con_filter => [
			consensus_results,
		],
	},
	mview_input => {
		mview_blast => [
			blast_output,
		],
	},
	hmmer_alig => {
		sreformat => [
			seqfile,
		],
		hmmbuild => [
			alignfile,
		],
		alistat => [
			multali_file,
		],
	},
	amps_blc_file => {
		alignfit => [
			blcfile,
		],
		aconvert => [
			blcfile,
		],
	},
	bipfile => {
		addquart => [
			bipfile,
		],
	},
	readseq_ok_alig => {
		druid => [
			sequences,
		],
		homology => [
			alignment,
		],
		prettyalign => [
			a2m,
		],
		clustalw_convert => [
			seqfile,
		],
		buildmodel => [
			alignfile,
		],
		clustalw => [
			infile,
		],
		dnapars => [
			infile,
		],
		tipdate => [
			alignment,
		],
		parciquart => [
			infile,
		],
		prot_nucml => [
			sequences,
		],
		distquart => [
			infile,
		],
		cosa => [
			alig,
		],
		fastdnaml => [
			alignment,
		],
		bambe => [
			data_file,
		],
		Puzzle => [
			infile,
		],
		dnadist => [
			infile,
		],
		protpars => [
			infile,
		],
		phyml => [
			alignment,
		],
		boxshade => [
			alignment,
		],
		decorate => [
			alignment,
		],
		filtersites => [
			infile,
		],
		protal2dna => [
			alig,
		],
		mview_alig => [
			alig,
		],
		readseq => [
			seq,
		],
		quicktree => [
			aligfile,
		],
		protdist => [
			infile,
		],
		fmtseq => [
			seq,
		],
		nnssp => [
			infile,
		],
		dsc => [
			seq,
		],
	},
	seqfile => {
		est2genome => [
			genome,
		],
		silent => [
			sequence,
		],
		btwisted => [
			sequence,
		],
		pestfind => [
			sequence,
		],
		patmatmotifs => [
			sequence,
		],
		stretcher => [
			asequence,
		],
		wordmatch => [
			asequence,
		],
		showorf => [
			sequence,
		],
		psiblast => [
			query,
		],
		genscan => [
			seq,
		],
		blast2 => [
			query,
		],
		etandem => [
			sequence,
		],
		extractcds => [
			infile,
		],
		diffseq => [
			asequence,
		],
		wobble => [
			sequence,
		],
		chaos => [
			sequence,
		],
		fasta => [
			query,
		],
		pepnet => [
			sequence,
		],
		bl2seq => [
			first_sequence,
		],
		pepwindow => [
			sequence,
		],
		maskseq => [
			sequence,
		],
		epestfind => [
			sequence,
		],
		needle => [
			asequence,
		],
		sixpack => [
			sequence,
		],
		digest => [
			sequence,
		],
		phiblast => [
			query,
		],
		hmmpfampar => [
			database,
		],
		water => [
			asequence,
		],
		pasteseq => [
			asequence,
		],
		backtranseq => [
			sequence,
		],
		psiblastpar => [
			query,
		],
		plotorf => [
			sequence,
		],
		extractseq => [
			sequence,
		],
		wublast2 => [
			query,
		],
		dotpath => [
			asequence,
		],
		einverted => [
			sequence,
		],
		recoder => [
			sequence,
		],
		isochore => [
			sequence,
		],
		megablastpar => [
			query,
		],
		octanol => [
			sequence,
		],
		megamerger => [
			asequence,
		],
		saps => [
			seq,
		],
		descseq => [
			sequence,
		],
		cutseq => [
			sequence,
		],
		merger => [
			asequence,
		],
		dotmatcher => [
			asequence,
		],
		pepwheel => [
			sequence,
		],
		prettyseq => [
			sequence,
		],
		wordcount => [
			sequence,
		],
		blastpar => [
			query,
		],
		rif => [
			query,
		],
		syco => [
			sequence,
		],
		banana => [
			sequence,
		],
		matcher => [
			asequence,
		],
		hmmpar => [
			database,
		],
		pepinfo => [
			sequence,
		],
		equicktandem => [
			sequence,
		],
		dottup => [
			asequence,
		],
		hmmpfam => [
			seqfile,
		],
	},

);

1;

