LOFT download page

Main program

The LOFT program for Windows can be downloaded below. In addition, we are working on an implementation in Java to make LOFT platform independent. The current, preliminary version of the Java classes, can be downloaded here as well.

LOFT paper (0.3 MB)
LOFT executable (0.4 MB)
Some remarks on the format of tree files (2 kB)
A preliminary Java version of LOFT (56 kB)

Supplemental material

In the paper "Orthology prediction at scalable resolution through automated analysis of phylogenetic trees" a benchmark is described that is based on gene families taken from COG. For each gene-family a phylogenetic tree was made, which is based on multiple sequence alignments. Both, the tree files, as well as the multiple sequence alignments can be downloaded using the links below. The LOFT analysis resulted in Orthology assignments which are also made available below. Finally, the benchmark requires information on gene-order. These data are described as COG_GeneNeighbors.

Benchmark based on gene-order conservation and COG-based gene-families

Multiple sequence alignments part 1 zipfile (16,8 MB)
Multiple sequence alignments part 2 zipfile (19,8 MB)
Multiple sequence alignments part 3 zipfile (8,3 MB)
Multiple sequence alignments part 4 zipfile (6,4 MB)
Multiple sequence alignments part 5 zipfile (3,4 MB)
Multiple sequence alignments part 6 zipfile (6,6 MB)
Treefiles zipfile (5.0 MB)
LOFT assignments zipfile (2.1 MB)
GeneNeighbors zipfile (2.1 MB)

Comparison using trusted species trees

Description of species numbers for gamma proteobacteria (662 bytes)
Species tree for gamma proteobacteria (165 bytes)
Zip file containing COG trees limited to the gamma proteobacteria (309 kB)
File containing node-statistics for both species tree reconciliation and default method of inference (31 kB)