Synopsis
Main usages
- treerecs -g GENETREE_FILE -s SPECIESTREE_FILE [-S MAP_FILE] [-t BRANCH_SUPPORT_THRESHOLD] […]
- treerecs -g GENETREE_FILE ‐‐info
Reconcile the gene tree(s) provided with -g with the species tree provided with -s
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
- EXPRESSION can be any colon-separated combination of the following:
- -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.
