This repository contains the scripts used during the analysis of the molecular innovations in the molecular stem lineage
The order of files is as follows:
filtering protein coding sequences:
- CDS_alternate.py
- NCBI_proteinisoforms.py
- NCBI_proteinisoforms_headers.py
- Ensembl_alternate.py
- Ensembl_pepfilter.py
CAFE analysis
- beforecafe.py
- filterresults.py
- expansionscontractions.py
- Heatmapfile.py
- CAFE_barplot_tree.py
Codeml
- Paml_orthogrouptonucleotide.py
- nucleotidetoamninoloop.py
- paml_removeinternalstops_nuc.py
- paml_removeinternalstops_pro.py
Protein domain annotations
- PFAM_mapping.py
- barplot_domain_percent.R
- Domain_acrchitecture.py