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UShER matUtils (version 0.2.1+galaxy0)

Mutation-annotated tree object:

Load a mutation annotated tree file, in protocol-buffers format (protobuf3).

matUtils mode:

Operation mode:

Select samples by explicitly naming them, one per line in a plain text file:

Remove the selected samples:

Remove the selected samples instead of keeping them in the output files

Select two representative samples per clade:

Toggle to automatically select two representative samples per clade currently included in the tree, pruning all other samples from the tree. Applies after other selection steps

Resolve all polytomies:

Resolve all polytomies by assigning branch length 0 relationships arbitrarily. Applied after selection; prevents recondensing of the MAT

Select the desired output:

Purpose

matUtils is a suite of tools used to analyze, edit, and manipulate mutation annotated tree (.pb) files.

matUtils Common Options

Extract: matUtils extract serves as a flexible prebuilt pipeline, and serves as the primary tool for subsetting and converting a MAT pb to other file formats. Sumary: matUtils summary is used to get basic statistics and attribute information about the mat. Annotate: matUtils annotate is a function for adding clade annotation information to the pb. Uncertainly: matUtils uncertainty calculates two specific metrics for sample placement certainty. These metrics can be very important to support contact tracing and reliable identification of the origin of a newly placed sample. Mask: matUtils mask is used to mask specific samples out of the pb, removing their mutations from visibility.

You can find more information in the matUtils official documentation page.