Keywords for Format Statement (Sequence Data)

Command

Setting

Remark

Example

DataType

DNA, RNA, nucleotide, protein

Specifies the type of data in the file

DataType=DNA

NSeqs

A count

Number of sequences

NSeqs=85

NTaxa

A count

Synonymous with NSeqs

NTaxa=85

NSites

A count

Number of nucleotides or amino acids

Nsites=4592

Property

Exon A protein-coding gene typically consists of multiple coding regions, known as exons, interspersed with non-coding DNA (introns), Intron Introns are the non-coding segments of DNA in a gene that are interspersed among the exons.,

Coding,

Noncoding,

and End.

Specifies whether a domain is protein coding. Exon A protein-coding gene typically consists of multiple coding regions, known as exons, interspersed with non-coding DNA (introns) and Coding are synonymous, as are Intron Introns are the non-coding segments of DNA in a gene that are interspersed among the exons. and Noncoding. End specifies that the domain with the given name ends at this point.

Property=cyt_b

Indel

single character

Use dash (-) to identify insertion/deletions in sequence alignments

Indel = -

Identical

single character

Use period (.) to show identify with the first sequence.

Identical = .

MatchChar

single character

Synonymous with the identical keyword.

MatchChar = .

Missing

single character

Use a question mark (?) to indicate missing data.

Missing = ?

CodeTable

A name

This instruction gives the name of the code table for the protein coding domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog. of the data

CodeTable = Standard