newick

Manipulate and draw trees in Newick format.

Downloads

Binary files are self-contained, no dependencies.

Linux newick
Windows newick.exe

Usage

Make a subset tree given file with leaf labels, one per line (labels
do not need to be a subtree, the tree is collapsed as needed):
    newick -input tree.newick -labels labels.txt -output subset.newick

Get leaf labels:
    newick -getlabels tree.newick -output labels.txt

Report miscellaneous information about a Newick file:
    newick -stats trees.newick

Calculate Robinson-Foulds (R-F) distance between two trees:
    newick -rofo tree1.newick -tree2 tree2.newick -log rofo.log

Calculate all-vs-all R-F distances between trees in Newick file:
    newick -rofos trees.newick -log rofos.log

Re-label trees, labels.tsv tab-separated with #1=old_label #2=new_label:
    newick -relabel trees.newick -labels labels.tsv -output relabeled_trees.newick

Add integer node number labels to internal nodes:
    newick -intlabel tree.newick -output intlabel.newick

Root by outgroup, specify labels.txt with leaf labels of outgroup or GroupName which
is a substring of the outgroup labels, e.g. phylum name if format is A1234.Phylum:
    newick trees.newick [-labels labels.txt | -outgroup GroupName] -output rooted.newick

Convert tab-separated to Newick:
    newick -tsv2newick tree.tsv -output tree.newick

Convert Newick to tab-separated:
    newick -newick2tsv tree.newick -output tree.tsv

Ladderize trees by rotating internal nodes so that larger subtree is always the 
left (default) or right subtree:
    newick -ladderize trees.newick -output ladderized.newick [-right]

Split tree into N roughly equal-sized subtrees (clusters), output is N files
named prefixi, i=1..N containing labels for each subtree:
    newick -split tree.newick -n N -prefix prefix

Convert trees to cladograms (leaves equidistant from root):
    newick -clado trees.newick -output clado.newick

Calculate edge confidence values from set of bootstrapped trees:
    newick -conf tree.newick -trees replicates.newick -output conftree.newick

Condense a tree by identifying best-fit nodes for each feature group and making
a tree of just those nodes; unary edges are collapsed by summing lengths and 
taking max confidence, leaves are labeled with features (e.g. phylum names):
    newick -condense trees.newick -features features.tsv -output condensed.newick

Extract just the branching order by collapsing unary nodes, deleting all edge lengths
and deleting all confidence values (all internal node labels removed):
    newick -topo trees.newick -output topos.newick

Delete one or more leaves and collapse any resulting unary nodes, useful e.g. for
deleting outgroup to simplify figure:
    newick -deleteleaves trees.newick [-label OutgroupName | -labels labels.txt] -output .newick

Draw one tree or several trees with optional coloring of edges:
    newick -draw tree.newick -svg figure.svg
    newick -drawf tree.newick -features features.tsv -colors colors.tsv -svg figure.svg
    newick -drawfs trees.newick -features features.tsv -colors colors.tsv -svg figure.svg

    -features is tsv file with #1 leaf_label #2 feature_name (e.g. phylum).
    -colors is tsv file with #1 feature_name #2 color, where color is any valid svg color,
      can be rgb, hex or name e.g. red.

    -default_color color
        Color for unlabeled edges (default gray).
    -title text
        Title text.
    -title_font_size n
        Title font size (default 10).
    -unitlengths 
        Treat all edge lengths as 1 (phylogram).
    -strokewidth n
        Line width for edges (default 1).
    -tree_width n
        Width of tree (default 1000).
    -tree_height n
        Height of tree (default 1000).
    -tree_spacing n
        Space between trees (default 300).
    -trees_per_row n
        Number of trees per row in figure (default 4).
    -triangles w,h
        Draw triangles at leaves with width w and height h.
    -legend legend.svg
        Legend showing features (e.g. phylum names) and colors.