Gotree: toolkit and api for phylogenetic tree manipulation

Commands

comment

This command modifies branch/node comments of input trees.

Please note that comments may be associated to nodes or to edges depending on where they are located in the newick representation. If the comment is located after branch length (i.e. :0.0011[edge comment], it will be associated to the branch. Otherwise, it will be associated to the node, i.e. (t1,t2)[node comment]:0.001[edge comment]).

If the tree has no branch lengths, it is not possible to differentiate them, thus all comments are associated to nodes.

Usage

Modify branch/node comments

Version:

Usage: gotree comment [command]

Available Commands: clear Removes node/tip comments transfer Transfers node names to comments

Flags: -h, --help help for comment -i, --input string Input tree (default "stdin") -o, --output string Cleared tree output file (default "stdout")

Global Flags: --format string Input tree format (newick, nexus, phyloxml, or nextstrain) (default "newick") --seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1) -t, --threads int Number of threads (Max=4) (default 1)

transfer subcommand

Usage: gotree comment clear [flags]

Flags: --edges-only Clear comments on edges only -h, --help help for clear --nodes-only Clear comments on nodes only

Global Flags: -i, --input string Input tree (default "stdin") -o, --output string Cleared tree output file (default "stdout")

clear subcommand

Usage: gotree comment transfer [flags]

Flags: -h, --help help for transfer --reverse

Global Flags: -i, --input string Input tree (default "stdin") -o, --output string Cleared tree output file (default "stdout")

#### Examples

* Removing node comments from an input tree

echo "(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);" | gotree comment clear --nodes-only

Should print:

(t1:1[e1],t2:1[e2],(t3:1[e3],t4:1[e4]):1[e5]);

* Removing edge comments from an input tree

echo "(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);" | gotree comment clear --edges-only

Should print:

(t1[n1]:1,t2[n2]:1,(t3[n3]:1,t4[n4]:1)[n5]:1);

* Removing all comments from an input tree

echo "(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);" | gotree comment clear

Should print:

(t1:1,t2:1,(t3:1,t4:1):1);

* Transfering node names to node comments:

echo "(t1:1,t2:1,(t3:1,t4:1)n5:1);" | gotree comment transfer

Should print:

(t1:1,t2:1,(t3:1,t4:1)[n5]:1);

* Transfering node comment to node name:

echo "(t1:1,t2:1,(t3:1,t4:1)[n5]:1);" | gotree comment transfer --reverse

Should print:

(t1:1,t2:1,(t3:1,t4:1)n5:1);