Sequence analysis

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The bioinformatics applications assigned the Biological domain Sequence analysis ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 23 results.

	Biological domain	Bioinformatics method	Input format	Output format
.NET BIO	Sequence analysis
BarraCUDA	Sequence analysis	Read mapping Sequence alignment	.fastq/.fq .fq.gz .bam	SAM
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.
Biopython	Sequence analysis Phylogenetics Population genetics Protein structure analysis	Sequence parsing	FASTA FASTQ GenBank ACE Nexus SFF PHD AB1 QUAL Blast output Phylip Clustalw EMBL Newick PIR	FASTA FASTQ GenBank Nexus SFF QUAL Phylip Clustalw EMBL Newick
BioSmalltalk	Sequence analysis Phylogenetics Population genetics Protein structure analysis	Sequence parsing	FASTA GenBank Nexus Blast output Phylip Clustalw EMBL	FASTA GenBank Nexus Phylip Clustalw EMBL
Blixem	Sequence analysis Phylogenetics	Sequence alignment visualisation	FASTA Blast output
DNA Chromatogram Explorer	Sequence analysis	File reformatting Chromatogram visualisation	FASTA GenBank ABI SCF TXT SEQ	FASTA SCF TXT SEQ
FAST: Fast Analysis of Sequences Toolbox	Genomics Sequence analysis	Sequence analysis Sequence parsing	GenBank Fasta/q Aligned Sequence Files	GenBank Fasta/q Aligned Sequence Files
Geneious	Sequence assembly (de novo assembly) Genomics RNA-Seq Metagenomics Epigenomics Structural variation Sequence analysis Phylogenetics Population genetics	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery	FASTA FASTQ SAM ELAND GenBank CSFASTA CSQUAL
GenomeBrowse	Sequence assembly (de novo assembly) Sequence alignment Whole genome resequencing Genomics Sequencing Sequence analysis Genetics Exome and whole genome variant detection Exome analysis Next Generation Sequencing	Visualisation Sequence assembly visualisation Sequence alignment visualisation	BAM
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
Lasergene	Sequence assembly (de novo assembly) Genomics SNP detection Indel detection Mapping Transcription factors and regulatory sites Sequence analysis Phylogenetics Protein structure analysis	Sequence assembly Read mapping Sequence alignment Peak calling Annotation Sequence analysis Scaffolding Sequence alignment analysis Chromatogram visualisation PCR primer design
Megraft	Metagenomics Sequence analysis Phylogenetics Community analysis Rarefaction	Sequence analysis	FASTA	FASTA
Metaxa	Metagenomics Sequence analysis Phylogenetics Community analysis	Sequence analysis Hidden Markov Model	FASTA	FASTA Tab-delimited file Summary
MirTrios	Genomics Sequence analysis De novo mutation detection	Read mapping Variant calling De novo mutation detection	VCF	BED
MotifLab	ChIP-seq Sequence motifs Transcription factors and regulatory sites Sequence analysis Gene regulation	Visualisation Peak calling Genome visualisation Sequence contamination filtering Sequence motif discovery Format conversion	FASTA GFF BED WIG CSV Delimited Text Others GTF Custom MEME Bioprospector Custom Motif format BedGraph Plain text BigWig Excel 2bit BigBed JASPAR XMS TRANSFAC	FASTA GFF BED WIG CSV Delimited Text HTML Others GTF Custom MEME Bioprospector Custom Motif format BedGraph Plain text Excel JASPAR XMS TRANSFAC
NCBI Genome Workbench	Sequencing Sequence analysis Sequence annotation Next Generation Sequencing	Visualisation Genome visualisation
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
Pipeline Pilot	Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq SNP detection RNA-Seq Sequence analysis Gene expression analysis Next Generation Sequencing	Read mapping Sequence alignment Sequence analysis Variant calling Comparative genomics Gene expression analysis	Velvet MUMmer Bowtie CisGenome MACS TopHat SAMtools BWA GATK Cufflinks Tablet BLAST MUSCLE BreakDancerMax CNV-seq FASTQC Integrative Genomics Viewer Mapreads MIRA3 SnpEff Tabix Artemis BioJava BioPerl ClustalW EMBOSS HMMER Jalview Primer3 PROSITE Sim4	Circos GBrowse2
SeqAn	Genomics Sequence analysis Phylogenetics		FASTA FASTQ SAM GFF	FASTA FASTQ SAM GFF
SequenceVariantAnalyzer	Genomics Personalised medicine Sequence analysis Genetic variation	Annotation SNP calling Genome visualisation	SAMtools HMMCNV	Sva
Spiral Genetics	Sequence assembly Whole genome resequencing SNP detection Mapping Sequence analysis Statistical calculation DNA-Seq Exome and whole genome variant detection Genomic assembly Quality control	Read mapping Sequence alignment File reformatting	FASTQ Fastq.gz	VCF 4.1
UGENE	Genomics Sequence analysis Phylogenetics Protein structure analysis	Sequence parsing	FASTA FASTQ SAM GFF Fasta.gz GenBank ACE AB1 Phylip Clustalw EMBL Newick Stockholm MSF	FASTA SAM Fasta.gz GenBank ACE Clustalw Newick Stockholm