From 49bc4d0b1bdd4d10210d2c59b800c8133d045cab Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 29 Jun 2012 19:31:08 +0000 Subject: [PATCH] Edited wiki page GSDI through web user interface. --- wiki/GSDI.wiki | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index 13c8c4e..27b1b7b 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -26,12 +26,17 @@ Must be in phyloXM format, with taxonomy and sequence data in appropriate fields ==== Species tree ==== Must be in phyloXML format unless option -q is used. -=== Options === +=== Output === + +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". + +=== Example === gsdi -g gene_tree.xml tree_of_life.xml out.xml -== Description == -Currently, GSDI strips the gene tree of nodes for which a matching species is not present in the species tree. == Reference == -- 1.7.10.2