Convergent evolution of NFP-facilitated root nodule symbiosis

<p># NFP</p> <p>Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."</p> <p>## 00_sequences<br>This directory contains NFP/LYR homologs and annotations.</p> <p>## 02_alignments<br>This directory contains NFP alignments</p> <p>## 03_trees<br>This directory contains gene trees and species tree guides for the analyses.</p> <p>## 04_reconciliation<br>This directory contains notung files and figures for the gene tree reconciliation analysis</p> <p>## 05_synteny<br>This directory contains files for the synteny analyses. The base directory contains circos plots and a subdirectory `Synteny.2.2020` containing scripts and summary output as well as the following:<br>### Results_Apr01.zip<br>Summary of synteny results<br>### csvs.zip<br>An archive containing all csvs in the analysis.<br>### fastas.zip<br>synteny analysis - chr 5 v 8.zip<br>### tsvs.zip<br>An archive containing all csvs in the analysis.<br>### blasts.zip<br>An archive containing blast results.<br>### coords.zip<br>An archive containing genome coordinate files.<br>### gffs.zip<br>An archive containing GFF annotations.<br>### gff3s.zip<br>An archive containing GFF annotations.<br>### imgs.zip<br>An archive containing figure files used for preparing the manuscript.<br>&nbsp;<br>## figs<br>This directory contains figure files used for preparing the manuscript.</p> <p>## Scripts_used_CF<br>This directory contains submission and shell scripts used to conduct the analyses.</p>