ALTree specifications


Unique identifier OMICS_13032
Name ALTree
Alternative name Association and Localisation tests using haplotype phylogenetic Trees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Results of haplotype reconstruction programs
Input format PHASE, FAMHAP
Output data Input file for the phylogeny reconstruction programs, the number of times a given haplotype is carried by case and control individuals
Output format PAUP, PHY, TXT
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.0
Stability Stable
PAUP, Phylip, PAML, PHYML, perl, gcc, make
Maintained No




No version available



This tool is not maintained anymore.

Publication for Association and Localisation tests using haplotype phylogenetic Trees

ALTree citations


An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

PMCID: 4478717
PMID: 25925750
DOI: 10.1186/s13058-015-0567-2

[…] ALTree also includes an algorithm used to identify which sites are the most likely ones to be involved in the association detected. For each short haplotype observed, the ALTree add-on altree-add-S ad […]


Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource

Breast Cancer Res
PMCID: 1413975
PMID: 16507150
DOI: 10.1186/bcr1377

[…] ogists who have helped us to collect fresh tissue, and the Pathology Services. We would particularly like to thank a dynamic group of research nurses who have worked for kConFab over the years (Meryl Altree, Carol Cameron, Helen Conlon, Bronwyn Culling, Vicky Fennelly, Janine Furmedge, Vivienne Geldard, Bronwyn Harris, Julie Kearney, Anna Nash, Kate Pope, Karen Robinson, Susan Schulz, Klaus Somers […]

ALTree institution(s)
Unité de recherche en Génétique Épidémiologique et structure des populations humaines, INSERM U535, Villejuif, France; Laboratoire Bordelais de Recherche en Informatique, UMR 5800, Bordeaux, France; Programme Avenir, INSERM U458, hôpital Robert Debré, AP-HP, Paris, France; Fondation Jean Dausset, Paris, France

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