Convergent evolution of NFP-facilitated root nodule symbiosis

# NFP

Scripts and data associated with the manuscript "Convergent evolution of NFP-facilitated root nodule symbiosis."

## 00_sequences
This directory contains NFP/LYR homologs and annotations.

## 02_alignments
This directory contains NFP alignments

## 03_trees
This directory contains gene trees and species tree guides for the analyses.

## 04_reconciliation
This directory contains notung files and figures for the gene tree reconciliation analysis

## 05_synteny
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:
### Results_Apr01.zip
Summary of synteny results
### csvs.zip
An archive containing all csvs in the analysis.
### fastas.zip
synteny analysis - chr 5 v 8.zip
### tsvs.zip
An archive containing all csvs in the analysis.
### blasts.zip
An archive containing blast results.
### coords.zip
An archive containing genome coordinate files.
### gffs.zip
An archive containing GFF annotations.
### gff3s.zip
An archive containing GFF annotations.
### imgs.zip
An archive containing figure files used for preparing the manuscript.
 
## figs
This directory contains figure files used for preparing the manuscript.

## Scripts_used_CF
This directory contains submission and shell scripts used to conduct the analyses.