TreeReconciliation

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
GeneTree	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
SDI		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
Softparsmap	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
gtp	0.15	Unix?	true	(same as for SDI? gtp is an implementation of the SDI algorithm in C)
Notung	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
RAP	NA	Java	false (RAP); true (RAP-masse)	binary gene tree? unresolved species tree takes support values into account	custom-modified Newick
RIO		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
prIMETV
EvolMAP	1.0	Java	command line and GUI available	binary species tree (newick) genome or gene sequences (fasta format)	Estimates paralogy and orthology Uses distances between genes and proceeds down species tree Gene trees can be extracted from lists of orthologs/paralogs/inparalogs Assumes genes are only lost or duplicated (no horizontal transfer) Fast algorithm designed for whole genome analysis