Release Notes

June 17 2026

• Added SVG export support for the compressed sequence-level view
• Improved performance for conservation histogram loading

June 11 2026

• An alignment of 137 bird assemblies from the Vertebrate Genomes Project (VGP) is now available in the Alignment Data menu
• SVG export support has been added for compressed gene-level and default sequence-level alignment views
• A new “Related tools” menu makes it easier to navigate from MCGV to other NCBI genome analysis tools
• Additional improvements and bug fixes

April 30 2026

• Gene track is now shown for anchor sequences in the compressed view
• Insertions between abutting aligned blocks are now displayed
• Additional minor improvements and bug fixes

March 30 2026

• You can now export an SVG image of the default alignment view
• The label column in the compressed view is now resizable, providing a more flexible layout
• Fungal datasets now display the species name and strain in the label column in compressed mode
• Additional minor improvements and bug fixes

January 21 2026

• All "Color by" options are combined into a single dropdown menu
• A new “Color by chromosome” option is now available, it helps visualize genome rearrangements, especially useful in compressed view
• Minor bug fixes, improvement to the search algorithm, and data updates are also included

December 29 2025

• An alternate compressed view of the alignments is now available that hides genes and minimizes space between assemblies
• You can now filter your view from the conservation table to show only alignments with or without particular mismatches, gaps, and insertions
• The MCGV URL now updates dynamically to capture both the coordinate range and the assemblies that are shown and hidden in your view

November 26 2025

• New alignments created at NCBI for Candidozyma and Cyptococcus fungi are now available to view
• FASTA downloads merge adjacent alignment segments to single lines in the file
• The alignment segment is briefly highlighted after you zoom to the segment in order to help situate you
• Additional minor bug fixes and data updates

September 25 2025

• An new alignment of 38 Lepidoptera species created by NCBI is now available to view
• You can now download up to 200 Kb of the alignment as a FASTA alignment
• Zoom to the range of an alignment segment using a link in the alignment info box
• Improvements to alignment and gene spacing
• Improved experience on mobile screens
• Additional data and UX improvements

August 21 2025

• Use the new search feature to go to a gene on the anchor assembly
• Switch chromosomes from the dropdown menu in the Chromosome overview panel
• Download an alignment FASTA file of the alignment sequence in view (up to 5 kb)
• Click on an insertion position to see an info box with the insertion coordinates and sequence
• Use the undo arrow to return to the previous view
• A new info banner highlights recent updates to the application
• Additional minor UX improvements

July 14 2025

• You can now choose to set any of the eight ape assemblies in the T2T ape alignment as the anchor assembly
• When you switch anchor assemblies, the view will remain at the same approximate zoom location on the genome alignment as it was before
• When you click on a number in the sequence conservation table, the corresponding data in the alignment rows is highlighted
  • When you click on a nucleotide position in the alignment, the corresponding location in the conservation table is highlighted
• Click on a gene model to see an info box with the gene name, description, and a button to zoom to gene
  • You can also double-click on a gene to zoom to its location
• The Sequence conservation panel is now open by default
• There's a graphical indicator when the Assembly alignment rows are loading data
• Additional bug fixes and minor UX improvements

May 27 2025

• You will now see nucleotide sequence when zoomed in to the maximal level
• A new legend at the sequence level describes the rendering for sequence matches, mismatches, gaps, and insertions
• Click on nucleotides in the alignment to see a popup with the coordinate position on the aligned assembly
• New sequence conservation table at maximal zoom level reports the numbers of assemblies with matches, mismatches, gaps, and insertions at each position in the alignment
• Click on a number in the conservation table to see a popup with a list of the assemblies with matches, mismatches, gaps, or insertions
• Additional bug fixes and style improvements

April 24 2025

• Use the new 'Switch anchor assembly' button to change the anchor assembly for the T2T ape genome alignment from human GRCh38.p14 to human T2T-CHM13v2.0
• Additional minor style and data improvements

April 15 2025

• An info popup reports the underlying assemblies for each bin in the sequence conservation graph
• Added an indicator when the sequence conservation graph is loading data
• Bug fixes in gene annotation

April 10 2025

• The eight-way primate alignment from the T2T consortium is now named 'T2T apes' in the application
• Bug fixes in gene annotation

March 27 2025

• Now showing intron and exon structures of annotated genes
• Gene annotation shown for all assemblies in the NHGRI primates alignment
• MCGV URL will update as you navigate in the application so that you can more easily share your precise view
• Comparative Genome Resource (CGR) banner added to bottom of page
• Bug fixes and data improvements to alignments and gene annotation

March 4 2025

• 'Filter assemblies' menu allows you to specify which taxa and assemblies are shown on the page
• Additional bug fixes and style improvements

February 20 2025

• Gene annotation is now displayed for EPO alignment assemblies for which annotation is available at NCBI. Annotation comes from RefSeq, or from the submitter if RefSeq annotation is not available
• Jagged ends are shown when the gene annotation is partial
• An arrow inside the gene indicates the gene orientation
• Click on a gene to zoom directly to it
• Additional bug fixes and data improvements

January 17 2025

• You can hide unaligned assemblies from the Sequence conservation graph

January 2025

• Multiple Comparative Genome Viewer (MCGV) is officially released!