evolbioinfo / booster-workflows

BOOSTER - BOOtstrap Support by TransfER - Workflows

This git repository contains the workflows used in the study "Boosting Felsenstein Phylogenetic Bootstrap".

They are implemented in Nextflow.

• Original data is located in the data folder:

  • mammals: Raw alignment and annotation file
  • ncbitax: Ncbi taxonomy
  • vih: Raw HIV pol alignment

• Each sub-folder corresponds to one analysis:

  • hiv_pol: analysis of 9147 sequences of hiv pol
  • mammals_COI5P: analysis of 1449 sequences of COI-5P protein in mammals;
  • mammals_simulated: analysis of simulated data;
  • bootstrap_simulated_bootstrap: Comparing bootstrap samples with Simulated samples from true tree
  • transfer_distance: analysis of transfer distance as a function of branch depth and number of taxa.

• All data described in the paper can be downloaded here.

Each folder contains a run.sh script to launch the analyses.

To run all the pipelines, the following dependencies are necessary:

• Nextflow

• booster

• goalign

• gotree

• PhyML 20120412

• FastTree 2.1.8

• raxmlHPC-PTHREADS v8.2.8

• python 2.x

• perl 5.x

• mafft 7

• R 3.2.3 with the following packages:

  • ape
  • big.phylo
  • reshape2
  • ggplot2

• jpHMM

• tqdist

• Seq-Gen

• INDELible