The University of Arizona

SICLE: Sister Clade Extractor

Dan DeBlasio(1) and Jen Wisecaver(2,3)

      (1) Department of Computer Science, University of Arizona,
      (2) Department of Ecology and Evolutionary Biology, Univeristy of Arizona,       (3) currently: Department of Biological Sciences, Vanderbilt University, Nashville, TN

SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy to use, adaptable, and high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. With SICLE it is possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. The program is a simple command line utility and is easy to adapt and implement in any phylogenetic pipeline. As a test case, we applied this new tool to published gene phylogenies to identify potential instances of horizontal gene transfer in Salinibacter ruber.

arXiv:1303.5785; v1 22 March 2013


Note that as of version 1.2 SICLE requires gcc version 4.6 or higher

Latest Release (v1.2)


v1.2 -- Tar Gzipped


Linux, x86-64 -- v1.2 -- Tar Gzipped
OSX -- v1.2 -- Tar Gzipped

Previous Versions (Source Only)

v1.0b -- Tar Gzipped
v0.7b -- Tar Gzipped

Development Trunk

GitHub (

Supplemental Information


The source tree files can for the case study of Salinibacter ruber are no longer available on, we have included the trees used in our case study here. (M8, tgz) (M13, tgz)

Renaming script mentioned on in the supplemental material of the paper (tgz)


Group Configuration File (txt)

Terms of Use

Creative Commons License
SiClE is free for noncommercial use under a Creative Commons Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, and comes with neither warranty nor guarantee. SiClE cannot be redistributed in any form without consent of the authors. If you wish to use SiClE for commercial purpose, you must first obtain the permission from all authors. All noteworthy uses of SiClE should cite the related paper above or this website.

Dan DeBlasio | Jen Wisecaver