From: cmzmasek@gmail.com Date: Fri, 29 Jun 2012 19:33:59 +0000 (+0000) Subject: Edited wiki page GSDI through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8afe7cf93b21387a16d2ff4ad522d784a7a02fc8;p=jalview.git Edited wiki page GSDI through web user interface. --- diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index 4d83100..13aa6ea 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -30,11 +30,11 @@ Must be in phyloXML format unless option -q is used. Besides the main output of a gene tree with duplications and speciations assigned to all of its internal nodes, this program also produces the following: * a log file, ending in `"_gsdi_log.txt"` - * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `_species_tree_used.xml` - * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish bases on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in '_gsdi_remapped.txt'. + * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `"_species_tree_used.xml"` + * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish bases on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in `"_gsdi_remapped.txt"`. === Example === -gsdi -g gene_tree.xml tree_of_life.xml out.xml +`gsdi -g gene_tree.xml tree_of_life.xml out.xml`