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This page contains a list of actively maintained software, that has been developed at BiRC. If you have any questions regarding a particular piece of software/wwwservice please contact the person responsible (listed to the right of each software description).

If you are employed at BiRC and want you software listed on this page, please contact Christian N. S. Pedersen.

WWW Services

FaBox FASTA online toolbox Palle Villesen Fredsted
PATBox P-type ATPase sequence classifier and database Dan Søndergaard
Pfold RNA 2nd structure prediction from a multiple alignment of RNA sequences. Zsuzsanna Sükösd
PhyFi Draws a phylogony from its Newick description. Jakob Fredslund
PriFii Finds primers from alignment. Jakob Fredslund


Phylogenetic analysis using a parsimony analysis that takes recombination events into account. Mikkel Heide Schierup
SAP Identification of species and other taxonomic units from DNA sequences Kasper Munch Terkelsen
SEQL-NRPS NRPS A-domain sequence classifier Dan Søndergaard

Downloadable Software

Blossoc Block-Association Mapping. Thomas Mailund
CoAnnealing Simulated Annealing Search for Coalescent Trees. Thomas Mailund
CoaSim Simulating the coalescent process. Thomas Mailund
GeneRecon A coalescent based tool for fine-scale association mapping. Thomas Mailund
HapCluster HapCluster is a software package for association mapping. Thomas Mailund
PPfold RNA 2nd structure prediction from a multiple alignment of RNA sequences. PPfold is an efficient implementation of the service Pfold available above. Zsuzsanna Sükösd
QDist Computation of the quartet distance between evolutationary trees. An old tool. Use tqDist instead. Christian N. S. Pedersen
QuickJoin A tool for fast canonical neighbor-joining tree construction but use RapidNJ instead. Thomas Mailund
RapidNJ A tool for fast canonical neighbor-joining tree construction. Christian N. S. Pedersen
SplitDist Split-Dist calculates the number of splits (edges) that differs for two trees. Thomas Mailund
tqDist Computation of the triplet- and Quartet-distance between evolutionary trees.  Christian N. S. Pedersen
zipHMM Library for very fast likelihood computations for hidden Markov models Christian N. S. Pedersen

Data Sets

HCmap Recombination map of the Human-Chimpanzee ancestor. Kasper Munch Terkelsen