Please refer to BitBucket Git repository for the newest version

• General description
• Downloads
• Old versions
• Changes
• The result of experiments
  • General info
  • Input files
  • The first experiment (by cost)
  • The second experiment (by voting)
• Bibliography

Urec is a software for computing unrooted gene and rooted species tree reconciliation, and inferring species phylogenies from sets of unrooted gene family trees based on results presented in [1,2].
Click here for the description of the software (this file is included in the packages below).

Unix v1.02 sources (run make to compile): urec102src.tgz
Windows executables v1.01 (console application; mingw compilation): urec101mingw.zip (soon version v1.02)

• urec101src.tgz

• v1.02 - improvements in random species/gene trees generator: -u and -E option

The sequences grouped into families taken from: http://cbi.labri.fr/Genolevures/. Unrooted gene trees computed by ClustalW. Species:

• c - C. glabrata
• k - K. lactis
• d - D. hanseni
• y - Y. lipolytica
• s - S. cerevisiae

The names of gene families (taken from Genolevures) and its unrooted gene trees: fam2gtrees.txt.

The sets of gene and species trees:

• strees.txt - the set of all 105 rooted species trees with leaves labeled by c,k,d,y and s.
• gtrees.txt - the set of 4807 unrooted gene family trees computed by ClustalW.

The summary of costs can be computed by:
    urec -b -S strees.txt -G gtrees.txt -cC
or in sorted version (in Unix with sort):
    urec -b -S strees.txt -G gtrees.txt -cC | sort -n -k2
To compute distributions of gene duplications and losses add "-d" option:
    urec -b -S strees.txt -G gtrees.txt -cCd
To obtain distributions shown as attributes in the nested parenthesis notation:
    urec -b -S strees.txt -G gtrees.txt -cCx
Results:

• result.txt - a file which contains 105 rooted species tree topologies sorted by the mutation cost (the first is the optimal species tree); each line contains:
  • number of the species tree
  • topology in nested parenthesis notation
  • mutation cost (dups+losses)
  • total number of duplications
  • total number of gene losses
• extended_result.txt - an extended version of the previous file; each line contains
  • mutation cost
  • a pair consisting of number of duplications and gene losses
  • a topology with attributes associated to each node; attributes define the distribution of gene dupl. and gene losses in the species tree
• extended_result.pdf visualization of extented_result.txt
• details - a directory containing 4708 ps-files (grouped into subdirs) one per each gene family; a file contains an optimal rooted gene tree and its embedding for the optimal species tree; note that only one is shown; other optimal rooted gene trees can be easily obtained by changing the topology of the hat; see [2] for more details
• A directory with all files

Computed by:
    urec -v -S strees.txt -G gtrees.txt
or in sorted version (in Unix with sort):
    urec -v -S strees.txt -G gtrees.txt -cC | sort -r -n -k2
Results (the points are not normalized): resultsvoting.txt

[1] Pawel Gorecki and Jerzy Tiuryn, URec: a system for unrooted reconciliation, Bioinformatics 2007 23(4):511-512
[2] Pawel Gorecki and Jerzy Tiuryn, Inferring phylogeny from whole genomes, Bioinformatics 2007 23: e116-e122 (Proc. of ECCB 2006)