svr_tree_to_html

    svr_tree_to_html [options] < tree.newick > tree.html

This script converts a newick tree into an HTML page. It has a rich set of options.

Introduction

usage: svr_tree_to_html [options] < tree.newick > tree.html

       -a   alias_file    - relabel tips using aliases        # table: [id alias]
       -b                 - show bootstrap/branch support values
       -bar               - show scale bar
       -c   tax|role|file - color tips by taxonomy, roles,
                            or groups specified in a file     # table: [id group]
       -d   desc_file     - add description to each tip       # table: [id description]
       -f   focus_list    - highlight a list of tips          # table: [id]
       -k   keep_list     - keep only the taxa listed         # table: [id]
       -l   link_file     - add URL to each tip               # table: [id URL]
       -lt  link_w_text   - add additional linked text        # table: [id text URL]
       -m   popup_file    - add simple mouseover to each tip  # table: [id popup]
       -nc  n_colors      - number of colors to use (D = 10)
       -p   g|s|file      - collapse trees by genus, species,
                            or groups specified in a file     # table: [id group]
       -s   show_list     - preferred tips to show when collapsing subtrees
                            (D = Woese' list of 69 common organisms)
       -t   title         - title for html page               
       -units label       - units label for scale bar; implies -bar
       -va  fa1[,fa2,..]  - vector annotation files    
       -x   min_dx        - minimum horizontal space between consecutive nodes (D = 1)
       -y   dy            - vertical separation of consecutive tips (D = 1)

       -anno              - use the annotator's SEED for URLs
       -gray n            - gray out name from the n-th word  # default: 2
       -pseed             - use PSEED
       -ppseed            - use PUBSEED
       -raw               - do not color or collapse tree,
                            may be superseded by -c and -p

Command-line options

-a alias_file

The sequence IDs in the FASTA file may not be what a user wants to see in the visualized tree. The alias file is a two-column table containing ID to alias mapping [ id alias ], and the tree tips will be relabeled with the aliases.

The alias file can also be used to supply a mapping from original sequence ID to FIG peg ID. With FIG ids, taxonomoy and function information can be automatically retrieved from the SEED server and painted to the tree tips.

-b

With the -b option, bootstrap values (or branch support values) are shown in percent for internal nodes of the tree. min_dx and dy are set to 2 unless they are explicitly specified.

-bar

Include a scale bar on the drawing.

-c tax | role | group_file

The value for the -c option can be a string ('tax' or 'role') or the name of a two-column table [ id, group ] that classifies the sequences into multiple groups. Correspondingly, the tips of the tree will be colord according to their major taxonomy group, functional role, or the customized group.

If tips are colored based on taxonomy groups, a taxonomy legend is shown. Otherwise, a table of color group (functional role by default) frequencies is shown.

The default behavior is to color tree tips by taxonomy groups.

-d description_file

A two-column table [ id, description ]. The description string will appear in parentheses after the sequence ID for each tip of the tree.

-f focus_list

A file with space-delimited IDs for sequences to be highlighted.

-k keep_list

Keep only the taxa listed (one per line) in the file keep.

-l link_file

A two-column table [ id, url ] for inserting URL for tree tips.

-lt linked_text_file

A three-column table [ id, text, url ] for inserting linked text for tree tips.

-m mouseover_file

A two-column table [ id, mouseover_description ]. The mouseover description string will appear in the popup box for the specified tip.

-nc n_colors

The number of colors to use for tree tips (D = 10). Max: 20.

-p g | s | group_file

This option provides a rule for collapsing subtrees whose tips all belong to the same group. The value for the -p option can be a string ('g' for genus, or, 's' for species), or the name of a two-column table [ id, group ] that classifies the sequenes into multiple groups.

The default behavior is to collapse subtrees whose nodes all belong to the same genus.

-s show_list (D = Woese' list of 69 common organisms)

Show a list of preferred tips when collapsing subtrees.

-t html_title

This title of the HTML page.

-units scale_bar_units

Include a scale bar with the specified units (inplies -bar).

-x n

Specifies the minimum length of a distance between two nodes. (D = 1)

-y n

Specifies vertical separation of consecutive tips. (D = 1)

-anno

With the -anno option, the tree tips will be linked to the annotator's SEED instead of the SEED viewer.

-gray n

Gray out the tip names after the n-th word. (D = 2)

-pseed

With the -pseed option, the taxonomy and function information is retrieved from the PSEED server. Setting the environment variable SAS_SERVER to 'PSEED' has the same effect.

-ppseed

With the -ppseed option, the taxonomy and function information is retrieved from the PUBSEED server. Setting the environment variable SAS_SERVER to 'PUBSEED' has the same effect.

-raw

Do not color or collapse the tree. This option maybe superseded if -c or -p is present.

Input

The input tree is a newick file read from STDIN.

Output

The output is a HTML page written to STDOUT.