Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' < https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.


Build Status Coverage Status

R implementation of the PhyLoTa sequence cluster pipeline. For more information see the accompanying website. Tested and demonstrated on Unix and Windows. Find out more by visiting the phylotaR website.

Install

Currently only the devlopment package is available:

devtools::install_github(repo='ropensci/phylotaR',
                         build_vignettes=TRUE)

Full functionality depends on a local copy of BLAST+ (>= 2.0.0). For details on downloading and compiling BLAST+ on your machine please visit the NCBI website.

Pipeline

phylotaR runs the PhyLoTa pipeline in four automated stages: identify and retrieve taxonomic information on all descendent nodes of the taxonomic group of interest (taxise), download sequence data for every identified node (download), identify orthologous clusters using BLAST (cluster), and identify sister clusters for sets of clusters identified in the previous stage (cluster^2) After these stages are complete, phylotaR provides tools for exploring, identifying and exporting suitable clusters for subsequent analysis.

phylotaR pipeline

For more information on the pipeline and how it works see the publication, phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

Running

At a minimum all a user need do is provide the taxonomic ID of their chosen taxonomic group of interest. For example, if you were interested in primates, you can visit the NCBI taxonomy home page and search primates to look up their ID. After identifying the ID, the phylotaR pipeline can be run with the following script.

library(phylotaR)
wd <- '[FILEPATH TO WORKING DIRECTORY]'
ncbi_dr <- '[FILEPATH TO COMPILED BLAST+ TOOLS]'
txid <- 9443  # primates ID
setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr)
run(wd = wd)

The pipeline can be stopped and restarted at any point without loss of data. For more details on this script, how to change parameters, check the log and details of the pipeline, please check out the package vignette.

library(phylotaR)
vignette("phylotaR")

Timings

How long does it take for a phylotaR pipeline to complete? Below is a table listing the runtimes in minutes for different demonstration, taxonomic groups.

Taxon N. taxa N. sequences N. clusters Taxise (mins.) Download (mins.) Cluster (mins.) Cluster2 (mins.) Total (mins.)
Anisoptera 1175 11432 796 1.6 23 48 0.017 72
Acipenseridae 51 2407 333 0.1 6.9 6.4 0.017 13
Tinamiformes 25 251 98 0.067 2.4 0.18 0.017 2.7
Aotus 13 1499 193 0.067 3.2 0.6 0 3.9
Bromeliaceae 1171 9833 724 1.2 28 37 0.033 66
Cycadidae 353 8331 540 0.32 19 18 0.033 37
Eutardigrada 261 960 211 0.3 11 1.8 0.05 14
Kazachstania 40 623 101 0.1 20 3 0.05 23
Platyrrhini 212 12731 3112 0.35 51 6.9 1.2 60

To run these same demonstrations see demos/demo_run.R.

License

MIT

Version

Version 1.

Authors

Dom Bennett (maintainer, R package dev), Hannes Hettling (workhouse code dev), Rutger Vos, Alexander Zizka and Alexandre Antonelli

Reference

Bennett, D., Hettling, H., Silvestro, D., Zizka, A., Bacon, C., Faurby, S., … Antonelli, A. (2018). phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. Life, 8(2), 20. DOI:10.3390/life8020020

Sanderson, M. J., Boss, D., Chen, D., Cranston, K. A., & Wehe, A. (2008). The PhyLoTA Browser: Processing GenBank for molecular phylogenetics research. Systematic Biology, 57(3), 335–346. DOI:10.1080/10635150802158688

ropensci_footer

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("phylotaR")

1.0.0 by Dom Bennett, 10 months ago


https://github.com/ropensci/phylotaR#readme


Report a bug at https://github.com/ropensci/phylotaR/issues


Browse source code at https://github.com/cran/phylotaR


Authors: Hannes Hettling [aut] , Rutger Vos [aut] , Alexander Zizka [aut] , Dom Bennett [aut, cre] , Alexandre Antonelli [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports igraph, rentrez, XML, ggplot2, sys, treeman, treemapify, R.utils

Depends on methods

Suggests testthat, knitr, rmarkdown

System requirements: BLAST+ (>=2.0)


See at CRAN