1. Casey Dunn
  2. Siebert_etal

Overview

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Sequence Analyses for Siebert at al. manuscript

This repository contains the data and scripts that were used to build the phylogenetic trees for:

Siebert, S, FE Goetz, SH Church, P Bhattacharyya, F Zapata, SHD Haddock, and CW Dunn. (preprint) Stem Cells in a Colonial Animal with Localized Growth Zones. bioRxiv preprint: doi:10.1101/001685</a>.

Contents

The included files are:

  • original_sequences.fasta, the newly sequenced genes for Nanomia bijuga. These will be submitted to NCBI.

  • nanos.fasta, piwi.fasta, and vasa_pl10.fas, fasta files of protein sequences included in the phylogenetic analyses.

  • analyses.sh, the shell script used to execute the analyses. It includes the SLURM job manager settings specific to our cluster, which can be deleted or modified for use on other clusters.

  • nanos.tre, piwi.tre, and vasa_pl10.tre, the trees that were produced by the analyses, with bootstrap support values. These trees are graphically presented in the manuscript as Supplementary Figure S2.