Short descriptions of the programs and modules included with TAMO are provided below. Click HERE to go back to the TAMO Homepage.

Routines for Import	Executable	File	Description
	X	GetDataFiles.py	Download support data files and routines over the internet.
X		HT.py	Load/Encapsulate/Slice High-throughput (genome-scale) datasets
X	X	MotifMetrics.py	Compute motif overrepresentation statistics among a sequence set, as compared to all sequences in a genome. Search of highest scoring k-mer motifs.
X		MotifTools.py	Kitchen-sink motif object
	X	Sitemap.py	Print ascii-maps of motif occurence among sets of sequences
X		DataSources/GO.py	Interface to Gene Ontologies, including statistical tests.
X		DataSources/Holstege.py	Interface to expression rate data from Holstege et. al.
X		DataSources/Novartis.py	Interface to GeneAtlas.
X		DataSources/PDB.py	A very simple PDB parser for 3-D protien/DNA structures
X		DataSources/SGD.py	Interface to the SGD yeast database, including genomic sequence.
X		DataSources/Yeast6kArray.py	Interface to the 6k intergenic array, including mappings from probes to genomic features.
X		Clustering/Kmedoids.py	K-medoids algorithms for motif clustering.
X		Clustering/MotifCompare.py	Utility routines for aligning and comparing motifs
X	X	Clustering/UPGMA.py	UPGMA algorithm for motif clustering.
X		MD/EM.py	Interface to C++ routines for MD via Expectation Maximization
X		MD/MDsupport.py	Wrapper for motif-related C++ routines
X	X	MD/MDscan.py	Interface to MDscan program.
X	X	MD/AlignAce.py	Interface to the AlignACE program.
X	X	MD/Meme.py	Interface to the MEME program.
X	X	MD/TAMO_EM.py	TAMO's very own EM implementation, that allows careful control over the seeds used for search.
	X	MDconvert/ace2tamo.py	Motif File Format Conversion Programs. The TAMO format is described here.
	X	MDconvert/kellis2tamo.py
	X	MDconvert/meme2tamo.py
	X	MDconvert/memeset2tamo.py
	X	MDconvert/tamo2table.py
	X	MDconvert/tamo2tamo.py
X		localpaths.py	Path information for TAMO
X		paths.py	More Path information for TAMO
	X	seq/Background.py	Compute high-order Markov background model from a collection of sequences.
X		seq/FakeFasta.py	Generate, seed, and randomly select sequences (for statistical testing.)
X		seq/Fasta.py	Fast Fasta IO
	X	seq/GenerateFastas.py	Generate a collection of sequence files from genome-wide data and sequence.
X		seq/Human.py	Fast, random-access interface to human sequence.
X		util/Arith.py	Several very useful arithmetic routines and statistical test (hypergeometric & bionomial)
X		util/PermuteTools.py	Routines for generating sequence permutations of k-mers. Useful for coarse-grained motif search (if fused with MotifMetrics.py)
X		util/Poisson.py	Poisson statistical tests and fitting routines to Poisson distributions
X		util/WMWtest.py	Wilcoxon / Mann-Whitney rank sum test
X		util/swilk.py	Shapiro-Wilk normality test (interfaces to underlying C++ routine)