This repository covers phylogenetic and regression analysis of 152 ABCE proteins from 76 plant species.
The full study is published in Frontiers in Genetics at https://doi.org/10.3389/fgene.2024.1408665.
In addition to the analysis scripts themselves, the repository also contains source data (alignments and annotations) and output trees.
- fasta/152 CDS FULL_correct.fas
- unaligned CDS sequences
- fasta/152_pepseq_MUSCLE.fa
- protein sequences, pre-aligned with MUSCLE
- ABCE_infosheet.tsv
- genome parameters and NCBI taxID for each species in the study
- annotation_v2.tsv
- annotations for each sequence used to construct phylogenies. Can be loaded into FigTree with the output trees from phylogenetic analysis
- prepare_alignments.sh
- abce_iqtree.sh
- creates sets of 20 CDS trees and 20 protein (pep) trees by running IQ-TREE with random seed values from 1 to 20 and otherwise identical parameters.
- abce_models_needskey.R
- trees/CDStrees.originals.seed1-seed20.nwk and trees/peptrees.originals.seed1-seed20.nwk
- Newick-formatted output trees from running abce_iqtree.sh, concatenated into two files with 20 trees in them (one for proteins, one for CDS). Trees are in the order of seed values used (1-20).
- Note that in Figtree the trees can be supplemented with annotations from the file annotation_v2.tsv
- trees/CDStrees.modified.figtree.nex and trees/peptrees.modified.figtree.nex
- Same 20+20 independently obtained trees, but saved with annotations as Figtree-openable .nex files, with the following modifications:
- Trees are in the order of their associated likelihood values (highest to lowest)
- All trees are rooted on the phylum Chlorophyta.
- Branches supported by less than 50% of bootstrap replicates are collapsed.
- Major phylogenetic clades are highlighted as on figures of the manuscript.
- Same 20+20 independently obtained trees, but saved with annotations as Figtree-openable .nex files, with the following modifications: