svr_sketch_tree

Introduction

    svr_sketch_tree [options]   < tree.nwk > tree.suitable.for.looking.at

This little utility invokes a tree "printing" utility Gary Olsen wrote. It has a rich set of options. We suggest a default usage of -m and -a. Thus, svr_sketch_tree -a -m < some_tree.nwk

is a reasonable thing to do.

Command-Line Options

-a

Specifies that you wish an aesthetic reordering of subtrees at each point.

-c

Asks that zero length branches be collapsed to multifurcating nodes.

-f=fasta.file

Read the fasta file to get comments associated with the tip IDs

-h

Specifies that the output should be written as HTML.

-i

This should only be used with a -f, and it means "print just the description, not the id followed by the description.

-l=file

The specified file should be a two-column, tab-separated table in which the first column is the sequence ID and the second the value you wish it to be relabeled to.

-m

The tree should be rerooted at a midpoint (take the longest distance between tips and reroot to the midpoint of that path)

-s

Do not include a scale bar in the diagram (but -S takes precedence)

-S bar_units

Include a scale bar with a units label in the diagram

-u

Make the output in UniCode line-drawing character set

-w=N

Allows you to specify the width you wish for the sketched tree

-x=N

Specifies the minimum length of a distance between two nodes

-y=N

Specifies vertical separation of consecutive tips