Monit, CPD;
Goldstein, RA;
(2018)
SubRecon: Ancestral Reconstruction of Amino Acid Substitutions Along a Branch in a Phylogeny.
Bioinformatics
, 34
(13)
pp. 2297-2299.
10.1093/bioinformatics/bty101.
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Abstract
SUMMARY: Existing ancestral sequence reconstruction techniques are ill-suited to investigating substitutions on a single branch of interest. We present SubRecon, an implementation of a hybrid technique integrating joint and marginal reconstruction for protein sequence data. SubRecon calculates the joint probability of states at adjacent internal nodes in a phylogeny, i.e. how the state has changed along a branch. This does not condition on states at other internal nodes and includes site rate variation. Simulation experiments show the technique to be accurate and powerful. SubRecon has a user-friendly command line interface and produces concise output that is intuitive yet suitable for subsequent parsing in an automated pipeline. AVAILABILITY AND IMPLEMENTATION: SubRecon is platform independent, requiring Java v1.8 or above. Source code, installation instructions and an example dataset are freely available under the Apache 2.0 license at https://github.com/chrismonit/SubRecon. CONTACT: c.monit.12@ucl.ac.uk
Type: | Article |
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Title: | SubRecon: Ancestral Reconstruction of Amino Acid Substitutions Along a Branch in a Phylogeny |
Open access status: | An open access version is available from UCL Discovery |
DOI: | 10.1093/bioinformatics/bty101 |
Publisher version: | https://doi.org/10.1093/bioinformatics/bty101 |
Language: | English |
Additional information: | Copyright © The Author(s) 2018. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
URI: | https://discovery.ucl.ac.uk/id/eprint/10044762 |
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