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>.
The included files are:
original_sequences.fasta, the newly sequenced genes for Nanomia bijuga. These will be submitted to NCBI.
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.
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.