diff --git a/README.md b/README.md index 86201f1..e4fe0b5 100644 --- a/README.md +++ b/README.md @@ -94,7 +94,7 @@ 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 @@ -102,9 +102,9 @@ Gotree [Docker image](https://hub.docker.com/r/evolbioinfo/gotree/) is usable fr ```[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: @@ -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 : ``` @@ -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