MEC-17-0853 Additional parameters/commands.
"Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries"
Balasingham KD, Walter RP, Mandrak NE, Heath DD.

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Commands for blastn of custom database:

We executed the following blastn command after using the list of species (see Supp. Table S1) to create a custom database:

blastn -db customdb -num_threads 24 -max_target_seqs 1 -outfmt "6 qseqid pident evalue stitle" -query eDNA_sequence_file.fasta -evalue 1E-60 -perc_identity 96 -out blasted_output.txt

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Commands for R cooccur package (Griffith et al. 2012):
The following commands use only one example, but note we implemented the same commands for all four presence/absence files (2 eDNA files for GR and SYD (Fig. 4A) and 2 capture-data files for GR and SYD (Fig. 4B)).

1. Load the files (convert eDNA sequence counts into presence/absence (1/0) data)
eDNA_GR <- read.csv("eDNA_GR_presabs.csv", header=T, row.names=1)

2. Run the cooccur algorithm
eDNA_GR_cooccur <- coccur(eDNA_GR, thresh=TRUE, spp_names=TRUE)

3. To plot the files individually
plot(eDNA_GR_cooccur, type="cooc") # this visualizes the cooccurrence as a pyramid

4. Create cooccurrence significance tables
eDNA_GR_table <- print(prob.table(eDNA_GR_cooccur))
write.table(eDNA_GR_table, "eDNA_GR_cooccurrence.txt", sep="\t")


Griffith DM, Veech JA, Marsh CJ (2016) cooccur: Probabilistic Species Co-Occurrence Analysis in R. Journal of Statistical Software, 69, 1-17.