Index    ◾    329

maximum likelihood 261

Mendel, Gregor 109

message passing interface see MPI

MetaBAT 304, 326

Metaeuk 104

Metagenome-Assembled Genome see MAG

metagenomics 253–254, 265, 301–302, 304, 326

methylation 213–214

microscopy 9

missense 109, 114, 143–145, 148, 150

molecular clock 261

motif 215–217, 225, 243–250

MPI 93

mpileup 79, 84, 114–116, 121, 123

MSA 146

multiple sequence alignment see MSA

multiplexing 5, 254, 270, 303–304, 306

N50 96, 102–103, 107

naïve Bayes 289, 291–293, 304

nanopore sequencing 9, 90

National Center for Biotechnology Information 50

Neanderthal 49

Needleman-Wunsch 55, 259

negative binomial 178–180, 185–189

NEWICK 298

NJ 177, 257, 261

nodes 56–57, 91–93

nonsense 110, 144, 148, 150

nonsynonymous codon 109, 146

normalization 174, 176, 182–183, 186–187

novoalign 65

nucleosome 213, 216

oligo 6, 8, 249

ONT 9–10, 90, 203, 239–240, 305

open reading frame see ORF

open-reference clustering 255, 278, 280, 282, 289,

301

operon 2, 164

ORF 2, 164, 325

ortholog 103–105, 108

overlap 81, 89–93, 107

overlap-consensus 90–91, 107

Oxford Nanopore Technologies see ONT

PacBio 9–10

Pacific Bioscience see PacBio

PairHMM 126

pairwise alignment 90–91, 107, 126, 259

Pandas 104

parsimony 261

PCoA 300

peak calling 215–217, 223

phosphorylation 213

phred 12–14, 23–24

PICARD 79, 86, 130, 132, 134–135, 210

Pielou’s Evenness 262

plants 49, 253

polymerase chain reaction 4

position-specific scoring matrix see PSSM

prefix tree 56

principal coordinate analysis see PCoA

prodigal 104, 323, 325–326

PSI-BLAST 146

PSSM 146

purine 1, 109, 247

pyrimidine 1, 109, 247

pyrophosphate 5–6

pyrosequencing 5–6

Q score 12–13

quasi-negative binomial 178–179, 196

QUAST 100–103, 107–108, 317–318, 326

rank table 62–63

RDP 258–259

RefSeq 50, 228, 311

regular expression 81

representative sequence 255, 258–261

ribonucleic acid see RNA

Ribosomal Database Project 258–259, 302

ribosome 2, 254

richness 261–262, 299

RIN 18

RNA integrity see RIN

RNA-Seq 163, 165–169

Robert Holley 3

Roche 454 5–7

RPKM 174–175, 210, 212

Samtools 53–54

Sanger, Frederick 3

Sanger sequencing 4, 90, 254

SARS-CoV-2 97, 99, 116, 118, 127, 155–157, 159–160

scaffold 89, 94–100, 102–103, 304–305, 316–320

seed-and-extend 65

seeding 73

SEPP 104

sequence alignment 53, 55, 63, 65, 70, 87, 90

sequencing depth 41, 45, 90, 114, 160, 175, 190

Shannon’s diversity index 261–262

sickle 305, 310, 325

SIFT 145–148, 152, 161

singleton 42, 46, 309

SMRT 9, 90, 98, 166