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
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