Here are the data structures with brief descriptions:

caferror
conf
mcl2rawcafe
Argument
ArrayList
ascii_visualization
BirthDeathCacheArray	A cache of values of family size transition probabilities
BirthDeathCacheKey
BranchCuttingParam
CafeFamily	Structure representing a matrix of values of family sizes
CafeFamilyItem	Represents a single gene family and the number of members of that family that exist in each species
CafeNode
CafeTree
CDParam
change
chooseln_cache	A cache of values of chooseln
ConditionalDistribution
coord
cross_validator
CutBranch
ErrorMeasure
errormodel_args
ErrorStruct
esterror_args
family_args
family_line_item
family_size_range
FMinSearch
gene_family
Globals
GMatrix
hash_table	Identifies the hashtable for which operations are to be performed
hash_table_element	Stores an hash table element for use in the hash table
input_values
io_error
lambda_arg_base
lambda_args
lambda_range
lambdamu_args
lhtest_args
load_args
log_buffer
LRT2LParam
LRTParam
my_ctype
newick_visualization
PnodeParam
poisson_lambda
posterior
probabilities
pvalue_args
Report
report_parameters
roots
square_matrix
String
svg_visualization
tagANOVA
tagANOVAResultElement
tagCafeParam	Singleton structure that holds all of the global data that Cafe acts on
tagHistogram
tagLinkedListItem
tagMetapostConfig
tagPhylogenyNode
tagTree
tagTreeNode
tagVector
to_lower
tree_visualization
viterbi_args
viterbi_parameters
ViterbiParam