HacDivSel: Detection of divergent selection





Citing HACDivSel
  • Carvajal-Rodríguez,A. 2017. HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations. PLOS ONE 12(4): e0175944. Doi: 10.1371/journal.pone.0175944.






This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. See the file "gpl.html" under the "license" directory.


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Program installation
You can download the adequate version of HacDivSel from the download menu at the left. The zip file includes the manual of the program jointly with the executables for Windows and Ubuntu and the source code with a Makefile for compilation for linux/MAC users. From the sources folder, the user can compile and install all source codes needed to run HacDivSel just by typing "make" from the linux console.
Program overview
HaCDivSel is a computer program designed to find signals of natural selection in the genome of populations that share polymorphisms. It combines haplotypic pattern information with population differentiation information and can be a useful tool for exploring divergent selection patterns when approximate knowledge of haplotype phase is available. Alternatively, HacDivSel also includes the EOS method, which is a useful outlier test when SNPs are independent.


The new, forthcoming version 1.5 also includes a haplotype-based method specifically dedicated to selection detection when a priori information on candidate sites is available


HacDivSel requires a sequence file. By default it accepts the ms format but Fasta, FastPhase, HapMap phased are also accepted as haplotype input files. In addition, Genepop, BayeScan and PLINK (MAP/PED) formats are accepted as files for outlier analysis.












A. Carvajal-Rodriguez - Departamento de Bioquímica Genética e Inmunología - Universidad de Vigo. ( Last update: July 2021)