alignment-filter.py: script used on automatically generated trimmed MSAs in fasta format that checks whether the alignment is long enough, if it contains sufficient number of taxa and discards sequences containing too many gaps, called by phylo-pipeline.sh

batchlast.sh: script used to get top LAST hits for a kareniacean seed sequence (p-value threshold 1E-5) and pull the sequences in fasta format into a single file

lastparser.sh: script for parsing LAST output file to extract IDs of the sequences to be used in phylogenetic analysis (five top hits for dinoflagellates, top hit for other), called by batchlast.sh

modASAFind.py: modified ASAFind script(original: https://bitbucket.org/rocaplab/asafind/src/main/) to be used with kareniacean-specific scoring matrix (scoringtable-kareniaceae.txt)

phylo-pipeline.sh: script covering the automatic phylogenetic pipeline, takes in homolog datasets in fasta format in a specified directory and passes them through several steps: 1) alignment by MAFFT, 2) trimming by Trimal, 3) check by alignment-filter.py, and 4) tree construction by IQ-Tree

scoringtable-kareniaceae.txt: scoring matrix for modified ASAFind

SP5toSP4.py: script used to reformat the output of Signalp 5.0 to the older format recognized by ASAFind

the treesorter script used for scoring and sorting the single gene trees based on the recovered topology (phylogenetic origin of the gene of interest they support) is available, along with a detailed manual and sample data, at: https://github.com/vanclcode/treesorter/