Pipeline release! nf-core/pairgenomealign v2.2.2 - nf-core/pairgenomealign v2.2.2 – Juicy!
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/2.2.2
#comparativegenomics #dotplot #genomics #last #pairwisealignment #synteny #wholegenomealignment #nfcore #openscience #nextflow #bioinformatics

Release nf-core/pairgenomealign v2.2.0 – Chagara ponzu · nf-core/pairgenomealign
v2.2.0 "Chagara ponzu" - [May 29th 2025]
Added
Support for export to BAM and CRAM formats (#31) (#43).
SAM/BAM/CRAM alignments files are sorted and their header features all sequences of the targe...
GitHub
Release nf-core/pairgenomealign v2.0.0 – Naga imo · nf-core/pairgenomealign
v2.0.0 "Naga imo" - [February 5th, 2025]
Breaking changes
The LAST software was updated and it has new defaults for some of its
parameters. The alignments ran with this pipeline will not be identi...
GitHub
Release nf-core/pairgenomealign v1.1.1 – Kani nabe · nf-core/pairgenomealign
This release brings the pipeline to the standards of Nextflow 24.10.1 and nf-core 3.1.0. No changes were made to the alignment process.
GitHubPipeline release! nf-core/pairgenomealign v1.1.0 - nf-core/pairgenomealign v1.1.0 – Nattou Maki!
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/1.1.0
#comparative-genomics #dot-plot #genomics #last #pairwise-alignment #synteny #whole-genome-alignment #nfcore #openscience #nextflow #bioinformatics

Release nf-core/pairgenomealign v1.1.0 – Nattou Maki · nf-core/pairgenomealign
Added a new softmask parameter, to optionally keep original softmasking.
GitHubPipeline release! nf-core/pairgenomealign v1.0.0 - nf-core/pairgenomealign v1.0.0 – Sweet Potato!
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/1.0.0
#comparative-genomics #dot-plot #genomics #last #pairwise-alignment #synteny #whole-genome-alignment #nfcore #openscience #nextflow #bioinformatics

Release nf-core/pairgenomealign v1.0.0 – Sweet Potato · nf-core/pairgenomealign
Initial release. Thanks again to my colleagues, collaborators, and the nf-core community.
nf-core/pairgenomealign is a bioinformatics pipeline that aligns one or more query genomes to a target gen...
GitHubReconstructing the
#TreeOfLife is a central goal in biology. @jlsteenwyk & Nicole King discuss the use of
#synteny for reconstructing the ToL and propose a roadmap for conducting rigorous & accurate synteny-based
#phylogenomic analysis
#PLOSBiology https://plos.io/3Vavczo
The promise and pitfalls of synteny in phylogenomics
Reconstructing the tree of life is a central goal in biology. This Essay discusses the use of synteny, an emerging phylogenomic marker, for reconstructing the tree of life and propose a roadmap for conducting rigorous and accurate synteny-based phylogenomic analysis.

A window into plant evolution: The unusual genetic journey of lycophytes
An international team of researchers has uncovered a remarkable genetic phenomenon in lycophytes, which are similar to ferns and among the oldest land plants. Their study, recently published in the journal PNAS, reveals that these plants have maintained a consistent genetic structure for over 350 million years, a significant deviation from the norm in plant genetics.
Phys.org