Jalview

Jul 20, 2023

Viewer and editor for multiple sequence alignments

Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages e.g. the EBI Clustalw server and the Pfam protein domain database and is also available as a general purpose alignment editor.

o Reads and writes alignments in a variety of formats o Gaps can be inserted/deleted using the mouse. o Group editing insertion deletion of gaps in groups of sequences. o Removal of gapped columns. o Align sequences using Web Services Clustal, Muscle… o Amino acid conservation analysis similar to that of AMAS. o Alignment sorting options by name, tree order, percent identity, group. o UPGMA and NJ trees calculated and drawn based on percent identity distances. o Sequence clustering using principal component analysis. o Removal of redundant sequences. o Smith Waterman pairwise alignment of selected sequences. o Web based secondary structure prediction programs JNet. o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images PNG or postscript EPS.



Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data