UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

SubRecon: Ancestral Reconstruction of Amino Acid Substitutions Along a Branch in a Phylogeny

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. Green open access

[thumbnail of Goldstein VoRbty101.pdf]
Preview
Text
Goldstein VoRbty101.pdf - Published Version

Download (195kB) | Preview

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
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
Downloads since deposit
82Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item