From 82b03a5055d448b37a020fce5739def33969ad22 Mon Sep 17 00:00:00 2001
From: Robert Edgar <robert@drive5.com>
Date: Thu, 4 Nov 2021 10:33:08 -0700
Subject: [PATCH] Update README.md

---
 README.md | 100 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 99 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2e9b7a4..044522e 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,100 @@
 # newick
-Manipulate and draw trees in Newick format
+Manipulate and draw trees in Newick format.
+
+## Downloads
+
+Binary files are self-contained, no dependencies.
+
+Linux [newick](https://github.com/rcedgar/newick/raw/main/binaries/newick)   
+Windows [newick.exe](https://github.com/rcedgar/newick/raw/main/binaries/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).
+        -legend legend.svg
+            Legend showing features (e.g. phylum names) and colors.