Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

LSX: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference

View ORCID ProfileCarlos Javier Rivera-Rivera, View ORCID ProfileJuan I. Montoya-Burgos
doi: https://doi.org/10.1101/220053
Carlos Javier Rivera-Rivera
University of Geneva
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Carlos Javier Rivera-Rivera
Juan I. Montoya-Burgos
University of Geneva
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Juan I. Montoya-Burgos
  • For correspondence: juan.montoya@unige.ch
  • Abstract
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Motivation: LS3 is a recently published algorithm to reduce lineage evolutionary rate heterogeneity, a condition that can produce inference artifacts in molecular phylogenetics. The LS3 scripts are Linux-specific and the criterion to reduce lineage rate heterogeneity can be too stringent in datasets with both very long and very short branches. Results: LSX is a multi-platform user-friendly R script that performs the LS3 algorithm, and has added features in order to make better lineage rate calculations. In addition, we developed and implemented an alternative version of the algorithm, LS4, which reduces lineage rate heterogeneity not only by detecting branches that are too long but also branches that are too short, resulting in less stringent data filtering. Availability: The LSX script LSx_v.1.1.R and the user manual are available for download at: https://genev.unige.ch/research/laboratory/Juan-Montoya .

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 16, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
LSX: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
LSX: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
Carlos Javier Rivera-Rivera, Juan I. Montoya-Burgos
bioRxiv 220053; doi: https://doi.org/10.1101/220053
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
LSX: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
Carlos Javier Rivera-Rivera, Juan I. Montoya-Burgos
bioRxiv 220053; doi: https://doi.org/10.1101/220053

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (996)
  • Biochemistry (1485)
  • Bioengineering (941)
  • Bioinformatics (6806)
  • Biophysics (2414)
  • Cancer Biology (1782)
  • Cell Biology (2518)
  • Clinical Trials (106)
  • Developmental Biology (1685)
  • Ecology (2556)
  • Epidemiology (1489)
  • Evolutionary Biology (5006)
  • Genetics (3603)
  • Genomics (4618)
  • Immunology (1159)
  • Microbiology (4228)
  • Molecular Biology (1618)
  • Neuroscience (10753)
  • Paleontology (81)
  • Pathology (236)
  • Pharmacology and Toxicology (407)
  • Physiology (553)
  • Plant Biology (1448)
  • Scientific Communication and Education (410)
  • Synthetic Biology (542)
  • Systems Biology (1870)
  • Zoology (258)