Treerecs options

Synopsis

Main usages

  • treerecs -g GENETREE_FILE -s SPECIESTREE_FILE [-S MAP_FILE] [-t BRANCH_SUPPORT_THRESHOLD] […]
  • Reconcile the gene tree(s) provided with -g with the species tree provided with -s

  • treerecs -g GENETREE_FILE ‐‐info
  • Print informations about the gene tree(s) provided with -g with a branch support diagram

Option details

  • -h or ‐‐help
    Print help, then exit
  • ‐‐usage
    Print usage, then exit
  • -V or ‐‐version
    Print version number, then exit
  • -v or ‐‐verbose
    Verbose mode. Causes Treerecs to print messages about its progress.
  • -Y or ‐‐superverbose
    Super-verbose (chatty) mode. Print even more messages than in verbose mode.
  • -g or ‐‐genetree GENETREE_FILE
    Input gene tree file.
    Contains the gene tree(s) to be processed
    Accepted formats: Newick, NHX or PhyloXML
  • -s or ‐‐speciestree SPECIESTREE_FILE
    Input species tree file.
    Contains the species tree to be used as reference
    Accepted formats: Newick, NHX or PhyloXML
  • -a or ‐‐alignments ALIGNMENTS_FILE
    Input alignement file.
    Contains the pll substitution model to use and, for each of the provided gene-trees, the path to the corresponding multiple alignment file.
  • -S or ‐‐smap SMAP_FILE
    Input gene-to-species mapping file.
  • -r or ‐‐reroot
    Find the best root according to the reconciliation cost.
  • -d or ‐‐dupcost VALUE
    Specify gene duplication cost.
  • -l or ‐‐losscost VALUE
    Specify gene loss cost.
  • -t or ‐‐threshold EXPRESSION
    -t or ‐‐threshold quantiles[N]
    Specify branch support thresholds to be used while contracting gene trees.

    • EXPRESSION can be any colon-separated combination of the following:
      • none: no contraction
      • all: contract all branches. The tree collapses into a single polytomy
      • VALUE: contract branches with support strictly lower than VALUE
      • VALUE+epsilon: (or VALUE+e): contract branches with support lower than or equal to VALUE
        example: treerecs -t 0.5+epsilon or treerecs -t 0.5+e
    • quantiles[N]: use several threshold values: none, all, and the quantiles dividing the branch supports into N groups
  • -n or ‐‐sample-size VALUE
    Number of solutions to output (default: 1).
    Since there can be an exponential number of solutions, Treerecs does not offer to output them all. Rather, it outputs randomly one or more solutions from a uniform distribution.
  • -N or ‐‐–tree-index VALUE
    Only consider the VALUE-th gene tree in the gene tree file.
  • -o or ‐‐outdir OUTPUT_DIR
    Output directory.
  • -O or ‐‐output-format FORMAT
    Specify output format(s).
    Valid formats: newick(default), nhx, phyloxml, recphyloxml, svg.
    Multiple output formats can be specified by using a colon-separated list of formats or by repeating the option.
    example: treerecs -O recphyloxml:svg or treerecs -O recphyloxml -O svg
  • -f or ‐‐force
    Force possible overwrite of existing files.
    Treerecs usually refuses to write to a non-empty directory. This options tells it to go for it, possibly overwriting existing files.
  • -C or ‐‐sep CHARACTER
    Specify separator character for species names embedded in gene names.
  • -p or ‐‐prefix Y/N
    Specify whether the species_name is a prefix of gene_name.
  • -P or ‐‐parallelize
    Run in parallel if possible.
  • -M or ‐‐save-map
    Save map(s) used during execution.
  • -q or ‐‐quiet
    Silent mode. Treerecs will print nothing to the terminal in this mode.
  • -C or ‐‐costs-estimation
    Estimate duplication and loss costs.
  • ‐‐info
    Print informations about genetree(s) with a branch support diagram.
  • ‐‐case-sensitive
    Use case sensitive mapping.
  • ‐‐ale-evaluation
    Compute ALE log likelihood for each solution.
  • ‐‐output-without-description
    Strip output from gene tree descriptions.
  • ‐‐fevent
    Create a file that summarizes orthology/paralogy relationships.

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