astralScoring.r
- processing scored tree from ASTRAL (with the option -t 4)
- creates a PNG image of the rooted ASTRAL species tree with pie charts on branches
- requirement: treeio
quartetsampling.r
- processing trees from quartet sampling (Pease et al., 2018)
- output trees are (1) modified with sed&grep and (2) plotted in R to resemble trees in publications
- requirements: devtools, phyloch, phytools
monophyly.R
- testing whether multiple groups are monophyletic in multiple trees
- loop over is.monophyletic function
- requirements: ape, phytools
cpDNA_mapping.sh
- BWA mapping of filtered reads from HybPhyloMaker to cpDNA reference
- consensus call with kindel
- combine sequences to single FASTA file
- requirements: bwa, samtools, kindel v.0.1.4
extractGBplastome.sh
- extract sequences (in FASTA format) from full plastome provided in GenBank format: (1) all features (CDS, tRNA, rRNA), separated to exons, (2) all sequences among them (introns, spacers)
- requires product.txt in some cases
BaseSpaceDownload.sh
- download FASTQ files from Illumina BaseSpace using API
- reports basic information about Illumina run
- requirements: GNU parallel, curl
PhyPartsMETA.sh
- creates PhyParts PieCharts plot for set of gene trees and a species tree (on MetaCentrum)
- optionally builds ASTRAL tree
- requirements: phyparts, phyparts piecharts, newick utilities
makeREsummary.sh
- calculate number of reads/proportion of all identified repeat types in RepeatExplorer cluster annotation file
- based on annotations in the 5th (automatic) or 7th (final) column