HAL-HAS version 1.0.9

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HAL-HAS version 1.0.9

HAL-HAS is a program package, comprising HAL-BU, HAL-TD, and HAS, that was written to allow users to infer an optimal model of evolution for a given data set, a given tree. We introduce a family of non-stationary and non-homogeneous mixture models that approximate the rate Heterogeneity Across Lineages (HAL) and the rate Heterogeneity Across Sites... more

Bioinformatics Bioinformatics Software

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HAS-HAS Software HAL-BU HAL-TD HAS Heterogeneity Across Lineages Heterogeneity Across Sites Bioinformatics


HAL-HAS code repository on GitHub


Vivek Jayaswal, Thomas K.F. Wong, John Robinson, Leon Poladian, Lars S. Jermiin; Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages. Syst Biol 2014; 63 (5): 726-742. doi: 10.1093/sysbio/syu036



HAL-HAS was developed as a result of a collaboration involving Lars S Jermiin and Thomas KF Wong (CSIRO Ecosystem Sciences) and Vivek Jayaswal, Leon Poladian, and John Robinson (School of Mathematics and Statistics at the University of Sydney). More specifically, for a given tree and data set: HAL-BU considers heterogeneity in the substitution process across lineages. It starts with the simplest model of evolution (i.e., one that has the same rate matrix on every edge in the tree). It then generates and compares increasingly complex models (i.e., different rate matrices on different edges in the tree) with the aim to identify the optimal model of evolution (i.e., one that neither over- or underestimates the complexity) HAL-TD considers heterogeneity in the substitution process across lineages. It starts with the most complex model of evolution (i.e., one that has a different rate matrix on each edge in the tree). It then generates and compares simples models with the aim to identify the optimal model of evolution HAS considers heterogeneity in the substitution process across sites. It starts with the result from HAL-BU, or HAL-TD, and a simple model of evolution where sites are divided into invariable sites and one set of variable sites. It then increases the sets of variable sites from 1 to 2, 3, 4, 5, and so forth, each time assessing the fit between the tree, model, and data, with the aim to identify the optimal model. The output is the inferred optimal model of evolution of the data for a given tree. For further details, see the manual, which is included with the software.

This software was developed by the bioinformatics and phylogenomics team in Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia.

GPLv3 Licence with CSIRO Disclaimer

CSIRO (Australia)

Jayaswal, Vivek; Wong, Thomas KF; Robinson, John; Poladian, Leon; Jermiin, Lars (2014): HAL-HAS version 1.0.9. v1. CSIRO. Software Collection.

All Rights (including copyright) CSIRO 2014.

The metadata and files (if any) are available to the public.

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Tested on Linux and MacOS




About this Project

CLSD Strategic: Solving Biodiversity Cha

We generate knowledge on the mechanistic links and synergistic interactions between landscape change, species invasions and native species resilience in terrestrial ecosystems. Working on both natural and agricultural systems, we undertake research and develop theory to underpin more effective policy and management actions for conservation, invasio... more

Bruce Webber

Bioinformatics Software

Bioinformatics software previously made available from the CSIRO ICT and Services website.


Vivek Jayaswal

Thomas KF Wong

John Robinson

Leon Poladian

Lars Jermiin

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