get_entity_AlignmentTree

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:

get_entity_AlignmentTree -a < ids > table.with.fields.added

would read in a file of ids and add a column for each filed in the entity.

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the id. If some other column contains the id, use

-c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Related entities

The AlignmentTree entity has the following relationship links:

Aligns ProteinSequence

Command-Line Options

-c Column

Use the specified column to define the id of the entity to retrieve.

-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.