Difference between revisions of "TreeReconciliation"

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Revision as of 13:33, 19 October 2007

Synopsis of available software

Notes
  • The material in this table is not necessarily correct and complete. Please help with additions and corrections.
  • Thanks are due to Christian Zmasek for providing the bulk of the information in this table.


Name (URL) Version OS Command line Input Output
<a href="http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html">GeneTree</a> 1.3.0 Mac OS 7.5 or later, Win 95/NT 4.0 or later false (GUI only)
  • binary gene tree
  • binary species tree(s)
  • both in Nexus formatted file
  • uses its own format to separate species from gene name information.
  • reconciled binary gene trees (in GUI) and associated binary species tree(s) scored according to the selected optimality criterion (Nexus format)
  • positions of duplications can be outputted as a separate file
<a href="http://www.phylosoft.org/forester/">SDI</a> Java true
  • binary gene tree in NHX format
  • binary species tree in NH or NHX format.
  • binary gene tree with duplication positions indicated by NHX tags
<a href="http://www.cbu.uib.no/~steffpar/softparsmap/">Softparsmap</a> 1.02 Java true
  • unresolved gene tree in NH format
  • unresolved species tree in form of NCBI taxonomy files
  • sequence information in 'darwin' database format (linkes sequences with species)
  • property file: contains parameters for program
  • takes support values into account
results are written to one or two files per family
<a href="http://loco.biosci.arizona.edu/gtp/gtp.html">gtp</a> 0.15 Unix? true (same as for SDI? gtp is an implementation of the SDI algorithm in C)
<a href=" http://goby.compbio.cs.cmu.edu/notung/">Notung</a> 2.5 Win, Unix, Max OS X true
  • binary gene tree in NH, NHX, or extended NHX format
  • unresolved species tree in NH, NHX, or extended NHX format
  • takes support values into account
  • gene tree with duplication information in NH, NHX or extended NHX format
<a href="http://pbil.univ-lyon1.fr/software/RAP/RAP.htm">RAP</a> NA Java false (RAP); true (RAP-masse)
  • binary gene tree?
  • unresolved species tree
  • takes support values into account
custom-modified Newick
<a href="http://www.phylosoft.org/forester/">RIO</a> Java (Perl) true
  • multiple binary gene trees
  • binary species tree
  • name for query
  • rio perl script allows to use precalculated pairwise distance for gene tree building, but is tied to Pfam
list of orthologs (and superorthologs, ultraparalogs) for query with support values
<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=AbstractPlus&list_uids=12855432">prIMETV</a>