{"id":270,"date":"2019-04-30T16:24:09","date_gmt":"2019-04-30T14:24:09","guid":{"rendered":"https:\/\/project.inria.fr\/treerecs\/?page_id=270"},"modified":"2020-06-15T14:49:03","modified_gmt":"2020-06-15T12:49:03","slug":"treerecs-options","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/treerecs\/treerecs-options\/","title":{"rendered":"Treerecs options"},"content":{"rendered":"<style type=\"text\/css\">\n  .option {\n    border:0px transparent;\n    padding: 2px 4px;\n    color: #c0341d;\n    background-color: #fbe5e1;\n    border-radius: 4px;\n    font-family: \"Menlo\", \"DejaVu Sans Mono\", \"Liberation Mono\", \"Consolas\", \"Ubuntu Mono\", \"Courier New\", \"andale mono\", \"lucida console\", monospace;\n    font-size: 80%;\n  }\n  .green-option {\n    border:0px transparent;\n    padding: 2px 4px;\n    color: #34c01d;\n    background-color: #e5fbe1;\n    border-radius: 4px;\n    font-family: \"Menlo\", \"DejaVu Sans Mono\", \"Liberation Mono\", \"Consolas\", \"Ubuntu Mono\", \"Courier New\", \"andale mono\", \"lucida console\", monospace;\n    font-size: 80%;\n  }\n  .blue-option {\n    border:0px transparent;\n    padding: 2px 4px;\n    color: #341dc0;\n    background-color: #e5e1fb;\n    border-radius: 4px;\n    font-family: \"Menlo\", \"DejaVu Sans Mono\", \"Liberation Mono\", \"Consolas\", \"Ubuntu Mono\", \"Courier New\", \"andale mono\", \"lucida console\", monospace;\n    font-size: 80%;\n  }<\/style>\n<h2>Synopsis<\/h2>\n<h3>Main usages<\/h3>\n<ul>\n<li>treerecs <span class=\"option\">-g GENETREE_FILE<\/span> <span class=\"option\">-s SPECIESTREE_FILE<\/span> <span class=\"option\">[-S MAP_FILE]<\/span> <span class=\"option\">[-t BRANCH_SUPPORT_THRESHOLD]<\/span> <span class=\"option\">[&#8230;]<\/span><\/li>\n<p>    Reconcile the gene tree(s) provided with <span class=\"option\">-g<\/span> with the species tree provided with <span class=\"option\">-s<\/span><\/p>\n<li>treerecs <span class=\"option\">-g GENETREE_FILE<\/span> <span class=\"option\">&#x2010;&#x2010;info<\/span><\/li>\n<p>    Print informations about the gene tree(s) provided with <span class=\"option\">-g<\/span> with a branch support diagram\n<\/ul>\n<p><!--\n\n<h3>Miscellaneous<\/h3>\n\n\n\n\n<ul>\n  \n\n<li>treerecs <span class=\"option\">-h<\/span> or <span class=\"option\">&#x2010;&#x2010;help<\/span><br \/>\n    Print help, then exit\n  <\/li>\n\n\n  \n\n<li>treerecs <span class=\"option\">-V<\/span> or <span class=\"option\">&#x2010;&#x2010;version<\/span><br \/>\n    Print version number, then exit\n  <\/li>\n\n\n  \n\n<li>treerecs <span class=\"option\">&#x2010;&#x2010;usage<\/span><br \/>\n    Print usage, then exit\n  <\/li>\n\n\n<\/ul>\n\n--><\/p>\n<h2>Option details<\/h2>\n<ul>\n<li><span class=\"option\">-h<\/span> or <span class=\"option\">&#x2010;&#x2010;help<\/span><br \/>\n    Print help, then exit\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;usage<\/span><br \/>\n    Print usage, then exit\n  <\/li>\n<li><span class=\"option\">-V<\/span> or <span class=\"option\">&#x2010;&#x2010;version<\/span><br \/>\n    Print version number, then exit\n  <\/li>\n<li><span class=\"option\">-v<\/span> or <span class=\"option\">&#x2010;&#x2010;verbose<\/span><br \/>\n    Verbose mode. Causes Treerecs to print messages about its progress.\n  <\/li>\n<li><span class=\"option\">-Y<\/span> or <span class=\"option\">&#x2010;&#x2010;superverbose<\/span><br \/>\n    Super-verbose (chatty) mode. Print even more messages than in verbose mode.\n  <\/li>\n<li><span class=\"option\">-g<\/span> or <span class=\"option\">&#x2010;&#x2010;genetree<\/span> GENETREE_FILE<br \/>\n    Input gene tree file.<br \/>\n    Contains the gene tree(s) to be processed<br \/>\n    Accepted formats: <a href=\"https:\/\/en.wikipedia.org\/wiki\/Newick_format\">Newick<\/a>, <a href=\"https:\/\/sites.google.com\/site\/cmzmasek\/home\/software\/forester\/nhx\">NHX<\/a> or <a href=\"http:\/\/www.phyloxml.org\/\">PhyloXML<\/a>\n  <\/li>\n<li><span class=\"option\">-s<\/span> or <span class=\"option\">&#x2010;&#x2010;speciestree<\/span> SPECIESTREE_FILE<br \/>\n    Input species tree file.<br \/>\n    Contains the species tree to be used as reference<br \/>\n    Accepted formats: <a href=\"https:\/\/en.wikipedia.org\/wiki\/Newick_format\">Newick<\/a>, <a href=\"https:\/\/sites.google.com\/site\/cmzmasek\/home\/software\/forester\/nhx\">NHX<\/a> or <a href=\"http:\/\/www.phyloxml.org\/\">PhyloXML<\/a>\n  <\/li>\n<li><span class=\"option\">-a<\/span> or <span class=\"option\">&#x2010;&#x2010;alignments<\/span> ALIGNMENTS_FILE<br \/>\n    Input alignement file.<br \/>\n    Contains the pll substitution model to use and, for each of the provided gene-trees, the path to the corresponding multiple alignment file.\n  <\/li>\n<li><span class=\"option\">-S<\/span> or <span class=\"option\">&#x2010;&#x2010;smap<\/span> SMAP_FILE<br \/>\n    Input gene-to-species mapping file.\n  <\/li>\n<li><span class=\"option\">-r<\/span> or <span class=\"option\">&#x2010;&#x2010;reroot<\/span><br \/>\n    Find the best root according to the reconciliation cost.\n  <\/li>\n<li><span class=\"option\">-d<\/span> or <span class=\"option\">&#x2010;&#x2010;dupcost<\/span> VALUE<br \/>\n    Specify gene duplication cost.\n  <\/li>\n<li><span class=\"option\">-l<\/span> or <span class=\"option\">&#x2010;&#x2010;losscost<\/span> VALUE<br \/>\n    Specify gene loss cost.\n  <\/li>\n<li><span class=\"option\">-t<\/span> or <span class=\"option\">&#x2010;&#x2010;threshold<\/span> EXPRESSION<br \/>\n      <span class=\"option\">-t<\/span> or <span class=\"option\">&#x2010;&#x2010;threshold<\/span> quantiles[N]<br \/>\n    Specify branch support thresholds to be used while contracting gene trees.<\/p>\n<ul>\n<li>EXPRESSION can be any colon-separated combination of the following:\n<ul>\n<li><span class=\"blue-option\">none<\/span>: no contraction<\/li>\n<li><span class=\"blue-option\">all<\/span>: contract all branches. The tree collapses into a single polytomy<\/li>\n<li><span class=\"blue-option\">VALUE<\/span>: contract branches with support strictly lower than VALUE<\/li>\n<li><span class=\"blue-option\">VALUE+epsilon<\/span>: (or <span style=\"font-style: italic;\">VALUE+e<\/span>): contract branches with support lower than or equal to VALUE<br \/>\n            example: <span class=\"green-option\">treerecs -t 0.5+epsilon<\/span> or <span class=\"green-option\">treerecs -t 0.5+e<\/span><\/li>\n<\/ul>\n<li><span class=\"blue-option\">quantiles[N]<\/span>: use several threshold values: <span style=\"font-style: italic;\">none<\/span>, <span style=\"font-style: italic;\">all<\/span>, and the quantiles dividing the branch supports into <span style=\"font-style: italic;\">N<\/span> groups<\/li>\n<\/ul>\n<\/li>\n<li id=\"sample-size\"><span class=\"option\">-n<\/span> or <span class=\"option\">&#x2010;&#x2010;sample-size<\/span> VALUE<br \/>\n    Number of solutions to output (default: 1).<br \/>\n    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  <\/li>\n<li><span class=\"option\">-N<\/span> or <span class=\"option\">&#x2010;&#x2010;&#8211;tree-index<\/span> VALUE<br \/>\n    Only consider the VALUE-th gene tree in the gene tree file.\n  <\/li>\n<li><span class=\"option\">-o<\/span> or <span class=\"option\">&#x2010;&#x2010;outdir<\/span> OUTPUT_DIR<br \/>\n    Output directory.\n  <\/li>\n<li><span class=\"option\">-O<\/span> or <span class=\"option\">&#x2010;&#x2010;output-format<\/span> FORMAT<br \/>\n    Specify output format(s).<br \/>\n    Valid formats: newick(default), nhx, phyloxml, recphyloxml, svg.<br \/>\n    Multiple output formats can be specified by using a colon-separated list of formats or by repeating the option.<br \/>\n    example: <span class=\"green-option\">treerecs -O recphyloxml:svg<\/span> or <span class=\"green-option\">treerecs -O recphyloxml -O svg<\/span>\n  <\/li>\n<li><span class=\"option\">-f<\/span> or <span class=\"option\">&#x2010;&#x2010;force<\/span><br \/>\n    Force possible overwrite of existing files.<br \/>\n    Treerecs usually refuses to write to a non-empty directory. This options tells it to go for it, possibly overwriting existing files.\n  <\/li>\n<li><span class=\"option\">-C<\/span> or <span class=\"option\">&#x2010;&#x2010;sep<\/span> CHARACTER<br \/>\n    Specify separator character for species names embedded in gene names.\n  <\/li>\n<li><span class=\"option\">-p<\/span> or <span class=\"option\">&#x2010;&#x2010;prefix<\/span> Y\/N<br \/>\n    Specify whether the species_name is a prefix of gene_name.\n  <\/li>\n<li><span class=\"option\">-P<\/span> or <span class=\"option\">&#x2010;&#x2010;parallelize<\/span><br \/>\n    Run in parallel if possible.\n  <\/li>\n<li><span class=\"option\">-M<\/span> or <span class=\"option\">&#x2010;&#x2010;save-map<\/span><br \/>\n    Save map(s) used during execution.\n  <\/li>\n<li><span class=\"option\">-q<\/span> or <span class=\"option\">&#x2010;&#x2010;quiet<\/span><br \/>\n    Silent mode. Treerecs will print nothing to the terminal in this mode.\n  <\/li>\n<li><span class=\"option\">-C<\/span> or <span class=\"option\">&#x2010;&#x2010;costs-estimation<\/span><br \/>\n    Estimate duplication and loss costs.\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;info<\/span><br \/>\n    Print informations about genetree(s) with a branch support diagram.\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;case-sensitive<\/span><br \/>\n    Use case sensitive mapping.\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;ale-evaluation<\/span><br \/>\n    Compute ALE log likelihood for each solution.\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;output-without-description<\/span><br \/>\n    Strip output from gene tree descriptions.\n  <\/li>\n<li><span class=\"option\">&#x2010;&#x2010;fevent<\/span><br \/>\n    Create a file that summarizes orthology\/paralogy relationships.\n  <\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Synopsis Main usages treerecs -g GENETREE_FILE -s SPECIESTREE_FILE [-S MAP_FILE] [-t BRANCH_SUPPORT_THRESHOLD] [&#8230;] Reconcile the gene tree(s) provided with -g with the species tree provided with -s treerecs -g GENETREE_FILE &#x2010;&#x2010;info Print informations about the gene tree(s) provided with -g with a branch support diagram Option details -h or &#x2010;&#x2010;help\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/treerecs\/treerecs-options\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":972,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-270","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/270","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/users\/972"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/comments?post=270"}],"version-history":[{"count":96,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/270\/revisions"}],"predecessor-version":[{"id":387,"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/pages\/270\/revisions\/387"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/treerecs\/wp-json\/wp\/v2\/media?parent=270"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}