Table 11 Software and URLs.

From: Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

Tool

Website

BUSCO

https://busco.ezlab.org/

RepeatMasker

http://www.repeatmasker.org/

RepeatModeler

http://www.repeatmasker.org/

AUGUSTUS

http://bioinf.uni-greifswald.de/augustus/

BRAKER2

http://exon.gatech.edu/GeneMark/braker1.html

GeneMark-ES

http://exon.gatech.edu/GeneMark/

Genscan

http://genes.mit.edu/GENSCAN.html

GlimmerM

http://www.cbcb.umd.edu/software/glimmerm/

SNAP

https://github.com/KorfLab/SNAP

BLAST+

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

BLAT

https://genome.ucsc.edu/FAQ/FAQblat.html; https://github.com/icebert/pblat

Diamond

https://github.com/bbuchfink/diamond

PASA

http://pasapipeline.github.io/

getorf

http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/getorf.html

RNAmmer

http://www.cbs.dtu.dk/services/RNAmmer/

SSR Finder

GenSAS custom tool, MainLab Bioinformatics

tRNAScan-SE

http://lowelab.ucsc.edu/tRNAscan-SE/

EVidenceModeler

http://evidencemodeler.github.io/

InterProScan

http://www.ebi.ac.uk/Tools/pfa/iprscan5/

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