Skip to content

Update README.md to reflect current functionalities #28

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
fredericlemoine merged 5 commits into from
Mar 13, 2026
Merged

Update README.md to reflect current functionalities #28

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
8334908
Initial plan
Copilot Mar 13, 2026
49dc32d
Update README.md to reflect current functionalities
Copilot Mar 13, 2026
50c8109
Update README.md
fredericlemoine Mar 13, 2026
747998d
Update README.md
fredericlemoine Mar 13, 2026
6382c3b
Update README.md
fredericlemoine Mar 13, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
100 changes: 55 additions & 45 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -94,17 +94,17 @@ Gotree Docker image is accessible from [docker hub](https://hub.docker.com/r/evo

```[bash]
# Display gotree help
docker run -v $PWD:$PWD -w $PWD -i -t evolbioinfo/gotree:v0.2.8b -h
docker run -v $PWD:$PWD -w $PWD -i -t evolbioinfo/gotree:v0.5.1 -h
```

### Singularity
Gotree [Docker image](https://hub.docker.com/r/evolbioinfo/gotree/) is usable from singularity . You may use it as following:

```[bash]
# Pull image from docker hub
singularity pull docker://evolbioinfo/gotree:v0.2.8b
singularity pull docker://evolbioinfo/gotree:v0.5.1
# Display gotree help
./gotree-v0.2.8b.simg -h
./gotree-v0.5.1.simg -h
```
### Conda
Gotree is also available on [bioconda](https://anaconda.org/bioconda/gotree). Just type:
Expand All @@ -114,7 +114,7 @@ conda install -c bioconda gotree
```

### From sources
To build gotree, you must first [download](https://golang.org/dl/) and [install](https://golang.org/doc/install) Go on your system ($1.21.6$).
To build gotree, you must first [download](https://golang.org/dl/) and [install](https://golang.org/doc/install) Go on your system ($1.24.11$).

Then you just have to type :
```
Expand Down Expand Up @@ -145,87 +145,97 @@ gotree implements several tree manipulation commands.
You may go to the [doc](docs/index.md) for a more detailed documentation of the commands.

### List of commands
* acr: Reconstruct most parsimonious ancestral characters
* annotate: Annotate internal nodes of a tree with given data
* asr: Reconstruct most parsimonious ancestral sequences
* brlen: Modify branch lengths
* add: Add the given length to all branches
* clear: Clear lengths from input trees
* cut: Cut branches whose length is greater than or equal to the given length
* round: Round branch lengths from input trees with a given precision
* cut: Cut branches whose length is greater than or equal to the given length
* round: Round branch lengths from input trees with a given precision
* scale: Scale lengths from input trees by a given factor
* setmin: Set a min branch length to all branches with length < cutoff
* setrand: Assign a random length to edges of input trees
* set: Assign a given length to edges of input trees
* setmin: Set a min branch length to all branches with length < cutoff
* setrand: Assign a random length to edges of input trees
* set: Assign a given length to edges of input trees
* collapse: Collapse branches or clades of input trees
* clades
* depth
* length
* support
* clade: Collapse a clade and replace it with a tip
* depth: Collapse branches having a given depth
* length: Collapse short branches of the input tree
* name: Collapse branches having given name or ID
* single: Collapse branches that connect single nodes
* support: Collapse lowly supported branches of the input tree
* comment: Modify branch/node comments
* clear: Remove node/tip comments
* clear: Remove node/tip comments
* transfer: Transfer node names to comments
* compare: Compare full trees, edges, or tips
* edges: Individually compare edges of the reference tree to a compared tree
* tips: Compare the set of tips of the reference tree to a compared tree
* trees: Compare 2 trees in terms of common and specific branches
* edges: Individually compare edges of the reference tree to a compared tree
* tips: Compare the set of tips of the reference tree to a compared tree
* trees: Compare 2 trees in terms of common and specific branches
* compute: Computations such as consensus and supports
* bipartitiontree: Builds one tree with only one given bipartition
* consensus: Compute the consensus from a set of input trees
* edgetrees: Write one output tree per branch of the input tree, with only one branch
* support: Compute bootstrap supports
* consensus: Compute the consensus from a set of input trees
* edgetrees: Write one output tree per branch of the input tree, with only one branch
* mutations: Extract the list of mutations along the branches of the phylogeny
* support: Compute bootstrap supports
* fbp ([Felsenstein Bootstrap](https://www.jstor.org/stable/2408678))
* tbe ([Transfer Bootstrap](https://www.nature.com/articles/s41586-018-0043-0))
* cut: Cut the tree
* date: Cut the input tree by keeping only parts in a date window
* divide: Divide an input tree file into several tree files
* download: Download a tree image from a server
* itol: download a tree image from iTOL, with given image options
* ncbitax: Download the full ncbi taxonomy in newick format
* panther: Download a tree from Panther database (http://pantherdb.org/)
* draw: Draw tree(s) with different layouts
* text: Display tree(s) in ASCII text format
* png : Draw tree(s) in png format, with normal, radial/unrooted or circular layout
* svg : Draw tree(s) in svg format, with normal, radial/unrooted or circular layout
* cyjs: Draw tree(s) in a html file, using cytoscape js
* generate: Generate random trees, branch lengths are simply drawn from an expontential(1) law
* download: Download trees or images from servers
* itol: Download a tree image from iTOL, with given image options
* ncbitax: Download the full ncbi taxonomy in newick format
* draw: Draw tree(s) with different layouts
* text: Display tree(s) in ASCII text format
* png: Draw tree(s) in png format, with normal, radial/unrooted or circular layout
* svg: Draw tree(s) in svg format, with normal, radial/unrooted or circular layout
* cyjs: Draw tree(s) in a html file, using cytoscape js
* generate: Generate random trees, branch lengths are simply drawn from an exponential(1) law
* balancedtree
* caterpillartree
* startree
* topologies: all possible topologies
* uniformtree
* yuletree
* graft: Graft a tree on an input tree in place of a given tip
* labels: Lists labels (names) of all tips
* ltt: Compute lineage through time data/plot
* graft: Graft a tree on an input tree in place of a given tip
* labels: Lists labels (names) of all tips
* ltt: Compute lineage through time data/plot
* matrix: Print (patristic) distance matrix associated to the input tree
* merge: Merges two rooted trees
* nni: Generate all NNI neighbors from a given tree
* prune: Remove tips of the input tree that are not in the compared tree, or that are given on the command line
* reformat: Convert input file between nexus and newick formats
* reformat: Convert input tree file between newick, nexus, and phyloxml formats
* newick
* nexus
* phyloxml
* rename: Rename tips of the input tree, given a map file, or a regexp, or automatically
* repopulate: Re populate the tree with identical tips (having the exact same sequence)
* reroot: Reroot trees using an outgroup or at midpoint
* midpoint
* outgroup
* rotate: Reorders neighbors of internal nodes. Does not change the topology, but just traversal order
* rand: Randomly reorders neighbors of internal nodes
* sort: Sort neighbors of internal nodes by ascending number of tips
* resolve: Resolve multifurcations by adding 0 length branches
* rotate: Reorder neighbors of internal nodes. Does not change the topology, but just traversal order
* rand: Randomly reorder neighbors of internal nodes
* sort: Sort neighbors of internal nodes by ascending number of tips
* rtt: Compute Root To Tip regression
* sample: Takes a sample (with or without replacement) from the set of input trees
* shuffletips: Shuffle tip names of an input tree
* subtree: extract a subtree
* support: Modify branch supports
* clear Clear supports from input trees
* round Round branch lengths from input trees with a given precision
* setrand Assign a random support to edges of input trees
* scale Scale branch supports from input trees by a given factor
* subtree: Extract a subtree
* support: Modify branch supports
* clear: Clear supports from input trees
* round: Round branch supports from input trees with a given precision
* setrand: Assign a random support to edges of input trees
* scale: Scale branch supports from input trees by a given factor
* stats: Print statistics about the tree, its edges, its nodes, if it is rooted, and its tips
* edges
* monophyletic : Print wether input tips form a monophyletic group in each of the input trees
* monophyletic: Print whether input tips form a monophyletic group in each of the input trees
* nodes
* rooted
* tips
* splits
* unroot: Unroot input tree
* upload: Upload a tree to a given server
* itol : Upload a tree to itol, with given annotations
* itol: Upload a tree to iTOL, with given annotations
* version: Display version of gotree

### Gotree commandline examples
Expand Down
Loading