recipe jalview

Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation.

Homepage

http://www.jalview.org/

License

GPL3

Recipe

/jalview/meta.yaml

Jalview is a free program for multiple sequence alignment editing, visualisation, analysis and figure generation. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. It is also able to import and annotate DNA and Protein products from VCF files and retrieve data and annotation from Uniprot, Ensembl, ENA, Rfam, Pfam and the PDBe.

package jalview

(downloads) docker_jalview

Versions
2.11.1.0-12.11.1.0-02.11.0-12.11.0-02.10.5-32.10.4-02.10.4b1-22.10.4b1-02.10.3-1

2.11.1.0-12.11.1.0-02.11.0-12.11.0-02.10.5-32.10.4-02.10.4b1-22.10.4b1-02.10.3-12.10.3-02.10.3b1-02.10.2b2-22.10.2b2-12.10.2b2-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install jalview

and update with:

conda update jalview

or use the docker container:

docker pull quay.io/biocontainers/jalview:<tag>

(see jalview/tags for valid values for <tag>)

Notes

This wrapper and installation is primarily for commandline-only use. Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to specify the java runtime if you need jalview to start up as quickly as possible Set JALVIEW_MAXMEM=2g to restrict jalviews maximal memory consumption (here to 2G RAM). Otherwise 90% of physical memory is allocated.