Phylogenetics

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

Definition:

Synonyms:

Query returned 20 results.

	Biological domain	Bioinformatics method	Input format	Output format
BBMap	Sequence alignment Whole genome resequencing RNA-Seq alignment SNP detection Metagenomics Phylogenetics Alternative splicing Resequencing Quality control Read binning	Read mapping Sequence alignment Sequence contamination filtering Sequence trimming RNA-Seq analysis	FASTA FASTQ SAM Scarf Paired FASTA+QUAL Interleaved Gzip	FASTA FASTQ SAM FASTA+QUAL Gzip
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
CANGS	Metagenomics Phylogenetics	Sequencing quality control Sequence trimming Primer removal
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
FaBox	Sequence assembly Phylogenetics
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
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
MG-RAST	Metagenomics Phylogenetics Metabolic reconstruction	Annotation	FASTA FASTQ SFF (Compressed) FASTQ (Compressed) FASTA	FASTA BIOM
MrBayes	Phylogenetics	Statistical calculation
MultiPSQ	Phylogenetics Microbial Surveillance Public health and epidemiology	Peak calling Classification Peptide mass fingerprint
Nesoni	RNA-Seq alignment SNP detection Phylogenetics	Sequence alignment	FASTA SAM
PyroNoise	Metagenomics Phylogenetics
RAST	Genomics Phylogenetics	Genomics Annotation
SeqAn	Genomics Sequence analysis Phylogenetics		FASTA FASTQ SAM GFF	FASTA FASTQ SAM GFF
Sequedex	Genomics Metagenomics Phylogenetics	Sequence analysis Sequence annotation	FASTA FASTQ	FASTA FASTQ Multiple hits per read
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