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.
Related entities
The AlignmentTree entity has the following relationship links:
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.