Browser Species

• SPECIES_TEMPLATE : To search for species or taxa containing one or several strings

  Enter here one or several strings, hit return or click on button OK. All species or taxon names containing this string will appear.

          Examples:
  homo sapiens
  vertebr
  root                             (allows to select the tree root)
  

  If one match only is found, the path in the tree through the node found will be given. All nodes placed under it in the species tree up to the currently selected Tree depth will also appear. If several matches are found, all of them are displayed. Click on one of them to make it the current node.

• CRE_LIST_IN_BROWSER : To create the list of sequences attached to the selected species .

  All sequences attached to the node displayed in reversed video, and to all nodes placed further down in the species tree, are selected.

• SP_PROF_SWITCH : To control the depth displayed down the tree starting from the current position in this tree

  When the currently selected Tree depth equals its maximum value, the tree is explored down to its end. This allows to get the complete species tree using the log treebutton.

• LOG_TREE : To write in the logfile currently displayed species or keywords

• CHOIX_SP_BROWSER : To change the current position within the species tree

  The current node of the species tree is displayed in reverse video.

  • Click on any displayed node to make it the new current node. The top line(s) of the form [ root; node; node;... ] gives the position in tree of the current node.
  • Click on this line(s) to go up one level in tree.
  • Use the Tree depth arrows to control how much to see down the current node.
  • Click on button Create seq. list to create the list of sequences attached to the current node or to any node further down in the tree. Any node prefixed by Synonym: may be used equally as the node above it to select the same sequences. Lines appearing within {} are taxon comments.

Browser Keywords

• KEYWORDS_TEMPLATE :To get all known keywords containing one or several strings
  • Enter one or several strings, hit return or click on button ok. All matching keywords will be displayed below.

    WARNING : very often the same meaning is written in many different ways!

  • Click on Create seq. list to create the list of sequences attached to all displayed keywords.
  • Click on Create list of matching keywords to put all displayed keywords in a keyword list. This list may then be edited using button edit list of the mainCurrent list window. Finally sequences attached to the edited keyword list can be selected using the proj. to seq. button in Selection operators panel.

• CRE_LIST _IN_BROWSER : To create the list of sequences attached to the selected keyword(s).

  All sequences attached to all displayed keywords are selected. Keywords are also partially tree-structured, so that some keywords indirectly select sequences attached to keywords placed further down in the tree.

• LIST_MATCHING_KEYWORDS : To create the list of all displayed keywords

  This list may then be edited using button edit list of the main Current lists window.

  To build the list of sequences attached to elements of the edited keyword list:

  1. Click on proj.to seqs. button in Selection Operatorspanel
  2. Click on previous list button in Selection Criteria and choose the desired keyword list
  3. Click on exec query

• LOG_TREE : To write in the logfile currently displayed keywords

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