File Format Compatibility Matrix

File format and software port compatibility matrix for bioSyntax.

Core Syntaxes

File Format	Description	sublime	vim	gedit	less	vscode
.fasta	Generic nt/aa sequence	X	X	X	X	X
.fastq	Fasta + PHRED quality	X	X	X	X	X
.clustal	Multiple Sequence Alignment	X	X	X	X	X
.bed	Genomic Ranges	X	X	X	X	X
.gtf	Genomic Annotation	X	X	X	X	X
.pdb	Protein Structure	X	X	X	X	X
.vcf	Variant Call Format	X	X	X	X	X
.sam	NGS Sequence Data	X	X	X	X	X

File Format	Description	sublime	vim	gedit	less	vscode
.fasta	fasta alternative AA colors
-	Clustal	X	-	X	-
-	Taylor	X	-	X	-
-	Zappo	X	-	X	-
-	Hydrophobicity	X	-	X	-
.fai	Fasta Index (faidx)	X	X	X	X	X
.flagstat	samtools flag summary	X	X	X	X	X
.cwl	Common Workflow Language	X	X	X	-	X
.wig	Wiggle data	-	-	X	-	X
.pdbx	Protein Structure (large)	-	-	-	-	-
.phylip	Multiple Sequence Alignment	-	-	-	-	-
.newick	Tree Format	-	-	-	-	-
.nexus	Phylogenetics data	-	X	-	-	-
.pml	Pymol Scripts	X	X	-	-	X
.ped	Plink Pedigree Format	-	-	-	-	-
.probam	Protein Bam	-	-	-	-	-
Psi Fasta	(http://www.psidev.info/peff)

File Format	Description	sublime	vim	gedit	less
.gaussian	Gaussian File (chemistry)	-	X	-	-