List of Abbreviations
- AFLP
- amplified fragment length polymorphism
- ASCII
- American Standard Code for Information Interchange
- BAC
- bacterial artificial chromosome
- BAM
- binary alignment/map
- BIC
- Bayesian information criterion
- BLAST
- basic local alignment search tool
- BWA
- Burrows–Wheeler algorithm
- BWT
- Burrows–Wheeler transformation
- cDNA
- complementary DNA
- CINEMA
- color interactive editor for multiple alignments
- cRNA
- complementary RNA
- dbGaP
- database of genotypes and phenotypes
- dbVar
- database of variation
- DDBJ
- DNA data bank of Japan
- DEG
- differentially expressed genes
- DNA
- deoxyribonucleic acid
- DP
- dynamic programming
- EMBL
- European Molecular Biology Laboratory
- EST
- expressed sequence tag
- ExPASy
- expert protein analysis system
- F81 model
- Felsenstein (1981) model
- FASTA
- fast all
- FDQN
- fully quantified domain name
- FPKM
- fragment per kilobase of exon per million mappable reads
- GATK
- genome analysis toolkit
- gi or GI
- gene identity
- GO
- gene ontology
- GOR
- Garnier, Osguthorpe, and Robson
- GSS
- genome survey sequence
- GTF
- gene transfer format
- GTR
- generalized time‐reversible
- GUI
- graphical user interface
- GWAS
- genome‐wide association studies
- HKY85 model
- Hasegawa, Kishino and Yano (1985) model
- IBL
- internal branch length
- InDels
- insertion and deletions
- INSDC
- International Nucleotide Sequence Database Collaboration
- IUPAC
- International Union of Pure and Applied Chemistry
- JALVIEW
- Java alignment viewer
- JC69 model
- Jukes and Cantor (1969) model
- K80 model
- Kimura (1980) model
- MACAW
- multiple alignment construction and analysis workbench
- MAFFT
- multiple alignment using fast Fourier transform
- ME
- minimum evolution
- MEGA
- molecular evolution and genetic analysis
- MISA
- microsatellite identification tool
- ML
- maximum likelihood
- MP
- maximum parsimony
- MSA
- multiple sequence alignment
- MSRE
- methylation sensitive restriction enzymes
- MUSCLE
- multiple sequence comparison by log‐expectation
- mYa
- million years ago
- NBRF
- National Biomedical Research Foundation
- NCBI
- National Center for Biotechnology Information
- NGS
- next‐generation sequencing
- NJ
- neighbor joining
- NWA
- Needleman–Wunsch algorithm
- ORF
- open reading frame
- OTU
- operational taxonomic unit
- PDB
- protein data bank
- pI/MW
- isoelectric point to molecular weight ratio
- PIR
- protein information resource
- PSD
- protein sequence database
- PWMs
- position weight matrices
- RCSB
- Research Collaboratory for Structural Bioinformatics
- RE
- restriction enzyme
- RF
- reading frame
- RFLP
- restriction fragment length polymorphism
- RPKM
- read per kilobase of exon per million mappable reads
- rRNA
- ribosomal RNA
- SAM
- sequence alignment/map
- SCOP
- structural classification of protein
- SIB
- Swiss Institute of Bioinformatics
- SNPs
- single nucleotide polymorphisms
- SPR
- subtree pruning regrafting
- SSR
- simple sequence repeats
- STS
- sequence‐tagged site
- SWA
- Smith–Waterman algorithm
- T92 model
- Tamura (1992) model
- TBR
- tree bisection reconnection
- T‐Coffee
- tree‐based consistency objective function for alignment evaluation
- TFBS
- transcription factor binding sites
- TFs
- transcription factors
- TIS
- translation initiation sites
- TN93 model
- Tamura and Nei (1993) model
- T‐P
- transversion‐parsimony
- TPA
- third‐party annotation
- TPM
- transcripts per million
- TRANSFAC
- transcription regulatory factors
- tRNA
- transfer RNA
- TTS
- triplex‐forming oligonucleotide target sequences
- uGDT
- unnormalized global distance test
- UniProt
- universal protein resource
- UPGMA
- unweighted pair group method with arithmetic mean
- URL
- uniform resource locator
- VCF
- variant call format
- VNTR
- variable number tandem repeat
- WGS
- whole genome shotgun
- wwPDB
- worldwide protein data bank
- YAC
- yeast artificial chromosome
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