schultzetal_coev_ant_fungus

This contains scripts used in the paper "The coevolution of ant-fungus agriculture" (working title), Schultz, et al., submitted.

Please cite this paper if you use these scripts.

.
├── PSSM
│   ├── README.md
│   ├── get-gff-subset.sh
│   └── pos-strand.sh
├── coding_analysis
│   ├── README.md
│   └── back_trans.py
├── probe_annotations_from_genomes
│   ├── README.md
│   ├── get_uniques.sh
│   ├── phyluce_probe_annotations_from_genomes
│   └── phyluce_probe_annotations_from_genomes_1.7.3
├── README.md
├── build_protein_annot_table.R
└── plot_dists_rev.R

• PSSM/: Contains scripts used for calculating a custom Position Specific Score Matrix (PSSM) for use with exonerate. See the README.md in that directory for more details.
• coding_analysis: Process of using exonerate to protein coding sequence from nucleotide UCE data. Includes steps to create coding alignments. See the README.md in that directory for more details.
• probe_annotations_from_genomes/: Contains phyluce_probe_annotations_from_genomes a modified version of phyluce_probe_slice_sequence_from_genomes from Phyluce 1.6.7 that, given a gff annotation file, returns annotations where UCE loci were mapped. In addition to phyluce 1.6.7, requires gffutils (version 0.9 for Python 2.7 used). See the README.md in that directory for more details. The file phyluce_probe_annotations_from_genomes_1.7.3 is the same script for phyluce 1.7.3.
• README.md: This file.
• build_protein_annot_table.R: Used to build a table of UCE and metadata for the associated metadata.
• plot_dists_rev.R: Compares alignments where the mafft feature --adjustdirection was enabled and disabled. It produces histograms of pairwise genetic distances of the aligned sequences highlighting sequences reverse complemented by mafft. Requires the R package seqinr. R 4.0.3 and seqinr 4.2_5 were used in the publication.