From: cmzmasek@gmail.com Date: Fri, 29 Jun 2012 19:45:36 +0000 (+0000) Subject: Edited wiki page GSDI through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dd976779b8df8db52359fe458b4ccccd94bdc52a;p=jalview.git Edited wiki page GSDI through web user interface. --- diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki index 928dbce..0f57750 100644 --- a/wiki/GSDI.wiki +++ b/wiki/GSDI.wiki @@ -27,6 +27,13 @@ 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. +=== 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 based 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"`. + === Taxonomic mapping between gene and species tree === GSDI can establish a taxonomic mapping between gene and species tree on the following three data fields: @@ -34,12 +41,7 @@ GSDI can establish a taxonomic mapping between gene and species tree on the foll * taxonomic identifiers (e.g. "35932" from uniprot or ncbi) * taxonomy codes (e.g. "PYRHO") -=== 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 based 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 -q gene_tree.xml tree_of_life.nwk out.xml`