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Gotree: toolkit and api for phylogenetic tree manipulation

Commands

reformat

This command reformats an input tree file into different formats.

So far, formats can be :

  • Input formats: Newick, Nexus, PhyloXML
  • Output formats: Newick, Nexus, PhyloXML.

The additionnal --translate option is available for gotree reformat nexus command. It replaces tip names by indices, and prints a translation table in the output nexus format.

Usage

General command

Usage:
  gotree reformat [command]

Available Commands:
  newick      Reformats an input tree file into Newick format
  nexus       Reformats an input tree file into Nexus format
  phyloxml    Reformats an input tree file into PhyloXML format

Flags:
  -f, --format string   Input format (newick, nexus, phyloxml, or nextstrain) (default "newick")
  -h, --help            help for reformat
  -i, --input string    Input tree (default "stdin")
  -o, --output string   Output file (default "stdout")

Examples

  • Reformat input nexus format into newick
gotree reformat newick -i input.nexus -f nexus -o output.nw
  • Reformat input newick format into nexus
gotree reformat nexus -i input.nw -f newick -o output.nexus
  • Reformat input phyloxml format into newick
gotree reformat newick -i input.xml -f phyloxml -o output.nw