sowhat – program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)

matemaker – make artificial mate pairs from long sequences for scaffolding

phyloconverge – an algorithm to look for convergent signals in phylogenetic trees

isoblat – use RNA transcripts to evaluate genome assemblies

exoblast – use sequence similarity to transcripts or protein sequences from a different species to evaluate genome assemblies

estimate genome size – scripts to estimate genome size and coverage from k-mer distributions

alien_index – identify potential non-animal transcripts in animal transcriptomes

FastqSifter – Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

leapfrog – identify “cryptic” BLAST hits between two datasets by employing a third intermediate dataset

JFR-Perl Modules – perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)