Comparative genomics

• DEBUGGING: BioPortal search
• DEBUGGING: BioPortal lookup

The bioinformatics applications assigned the Biological domain Comparative genomics ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 18 results.

	Biological domain	Bioinformatics method	Input format	Output format
BioNumerics	Sequence assembly Whole genome resequencing Genotyping Sequence analysis Comparative genomics Quality control Workflows Data handling Microbial Surveillance Epidemiology	Sequence assembly Read mapping Sequence alignment Annotation Genome visualisation Variant calling Comparative genomics Workflows	FNAQual .bam (C)FAST(A/Q) Compressed fastq .ab1 And many others.
BLAST Ring Image Generator	Comparative genomics	Visualisation Sequence assembly visualisation
Circos	Comparative genomics	Visualisation
DIAL	SNP detection Comparative genomics
DiscoSnp	Sequence assembly (de novo assembly) Sequencing Genotyping Comparative genomics High-throughput sequencing Population Genomics	Sequence assembly (de-novo assembly) Read depth analysis	FASTQ Fasta Compressed fasta Compressed fastq	Fasta
Easyfig	Comparative genomics	Comparative genomics	FASTA GenBank	SVG Bmp
ERGO Genome Analysis and Discovery System	Transcriptomics Metagenomics Transcription factors and regulatory sites Phylogenetics Comparative genomics SNP Functional genomics Gene structure Exome analysis Genome Wide Association Studies Metabolic pathways	Sequence alignment SNP detection SNP annotation Gene expression analysis Pathway or network analysis Sequence annotation Sequence functional annotation Metabolic network modelling
FHiTINGS	Metagenomics Comparative genomics	Sequence alignment
Galaxy	Sequence assembly Whole genome resequencing Genomics Comparative genomics Functional genomics	Sequence assembly Sequence alignment Visualisation Sequencing quality control
GenomeView	Genomics Transcriptomics Sequencing Sequence analysis Comparative genomics Quality control	Visualisation Data retrieval Genome visualisation Sequence alignment visualisation Plotting and rendering	FASTA BAM GFF BED WIG Blast output Clustalw EMBL (Compressed) FASTA GTF Multi-fasta BEDGraph	Gff3 Embl
KBASE	Comparative genomics	Annotation
Kissnp	Transcriptomics SNP detection Indel detection Comparative genomics	Sequence assembly Sequence assembly (de-novo assembly) Data retrieval	FASTA	FASTA
LAST	Genomics Comparative genomics	Sequence alignment	FASTA
Omixon Variant Toolkit	SNP detection Indel detection Mapping Sequence analysis Comparative genomics	Sequence assembly Read mapping Sequence alignment	FASTQ SAM CSFASTA Most others	SAM GFF VCF
SeqSphere+	Comparative genomics Microbial Surveillance	Sequence assembly Read mapping Variant calling	FASTA BAM GenBank ACE ABI SCF FASTA+QUAL	FASTA BAM ACE SCF
Sim4cc	RNA-Seq alignment Comparative genomics	Read mapping
Syapse	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	VCF
Tablet	Genomics Genotyping Comparative genomics	Sequence assembly visualisation	FASTA FASTQ SAM BAM MAQ SOAP ACE AFG VCF GTF GFF3	PNG