Glossary

tids

New reference identifiers or unique Taxon identifiers

rids

Old reference identifiers or Redundant taxon identifiers

subs

Refer to any number of inherited subordinate taxa that make a single tid

hdf5

Hierarchical Data Format 5. For details refer to HDF5

MSA

Multiple Sequence Alignment

MRCA

Most Recent Common Ancestor

16S

16S ribosomal RNA

IUPAC

International Union of Pure and Applied Chemistry

rRNA

ribosomal RNA

NCBI

National Center for Biotechnology Information

API

Application Programming Interface

taxid

Taxon identifier in NCBI database

spec

In PhyloMAF “spec” refers to set of stepwise instructions(or specifications) that define a pipeline(or pipe)

docker

In PhyloMAF “docker” refer to any intermediate data instance that moves in or out pipe specs

mediator

In PhyloMAF “mediator” refer to any class from mediators module that is responsible for providing mediator interface for the client database.

factor

In PhyloMAF “factor” refer to any class from factors module that describe the type of data to be mined.

singleton

In PhyloMAF “singleton” refer to any instance of the class from dockers module that contain actual data and not nested instances of type(self) of the docker.

tab

Refers to Total Ambiguous Bases within single sequence