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all_entities_AlignmentTree

Return all instances of the AlignmentTree entity.

An alignment arranges a group of protein sequences so that they match. Each alignment is associated with a phylogenetic tree that describes how the sequences developed and their evolutionary distance. The actual tree and alignment FASTA are stored in separate flat files. The Kbase will maintain a set of alignments and associated trees. The majority of these will be based on protein sequences. We will not have a comprehensive set but we will have tens of thousands of such alignments, and we view them as an imporant resource to support annotation. The alignments/trees will include the tools and parameters used to construct them. Access to the underlying sequences and trees in a form convenient to existing tools will be supported.

Example:

    all_entities_AlignmentTree -a 

would retrieve all entities of type AlignmentTree and include all fields in the entities in the output.

The AlignmentTree entity has the following relationship links:

Aligns ProteinSequence

Command-Line Options

-a

Return all fields.

-h

Display a list of the fields available for use.

-fields field-list

Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:

alignment_method
alignment_parameters
alignment_properties
tree_method
tree_parameters
tree_properties

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.